in the formation of mram devices , the alignment of mtj stacks to the metal line underneath poses a particularly tricky problem since the mtj stack itself is opaque . proper alignment , which is achieved through the use of a lithographic stepper prior to printing of the pattern , is based on the reflection of light / laser from the alignment structures etched on the layer underneath . the position of the alignment marks is calculated and the wafer is thus positioned accurately on the stage by the stepper feedback mechanism . however , because the mtj stack materials are opaque , this does not allow the stepper to otherwise “ see ” these alignment marks . accordingly , one way this problem has been addressed in the past is through the creation of surface topography with the alignment marks , as discussed above , in order to align opaque junctions . the formation of such alignment marks with topographic characteristics is typically implemented by etching out copper alignment marks using a tantalum nitride ( tan ) hardmask , followed by removal of the tan by chemical mechanical polishing ( cmp ), and deposition of the magnetic stack and hardmask layers . the resultant topography on the mtj stack is employed for alignment . again , this approach may result in slurry trapping in the alignment marks during prior tan cmp , thus making alignment rather difficult . referring initially to fig1 , there is shown a cross sectional view of a portion of processing of an mram device prior to an alignment step in which a conductive hardmask is aligned to lower level conductors . in the example depicted , the lower metal level represents the m2 wiring level of an fet - based mram . in the conventional alignment mark scheme shown in fig1 , a set of alignment marks 102 and associated overlay boxes 104 ( collectively referred to hereinafter as “ alignment marks ” 106 or simply “ marks ”) are formed in a dielectric layer 108 , along with lower metal lines 110 . an interlevel dielectric ( ild ) layer 112 is formed over the alignment marks , for the formation of a strap via ( not shown in the figures for purposes of simplicity , which connects the m2 metal lines to a corresponding lateral strap of the fet mram device ). an optically transparent layer 114 ( such as ta / tan , for example ) is formed over the ild layer 112 prior to deposition of the opaque mtj stack layer , collectively shown as 116 . then , a relatively thick conductive hardmask layer 118 ( e . g ., titanium nitride ( tin )) is formed atop the mtj stack layer 116 . in accordance with the previously described technique ( u . s . pat . no . 6 , 933 , 204 ), a portion of the hardmask layer 118 and mtj stack layer 116 above the alignment marks 106 is opened by a block mask , as shown in fig2 . this opening 119 allows the marks 106 to be visible by lithography equipment through the optically transparent layer 114 and ld layer 112 . in this manner , a tunnel junction reticle may be aligned to the m2 wordlines 110 in the tunnel junction lithographic process . as shown in fig3 , an antireflective ( arc ) layer 120 and photoresist 122 ( both optically transparent ) cover the partially excavated alignment mark site , protecting the transparent layer 114 and alignment marks 106 from further etching during the definition of the tunnel junction hardmask . however , since the mtj stack material 116 beneath the metal hardmask 118 is sputtered in a hot cathode during the patterning thereof , such a process would lead to resist reticulation and impregnation of any resist 122 by the magnetic material being sputtered from the field area . thus , to prevent this occurrence , the resist layer 122 and arc layer 120 are stripped immediately after the metal hardmask etch . the resulting hardmask pattern is then transferred to a top portion of the magnetic stack underneath by a subsequent etch , as shown in fig4 . from this point forward , there is no longer any material masking / protecting the partially excavated m2 alignment mark site 124 . accordingly , during the mtj stack sputter , during the partial mtj etch , or during a subsequent strap etch where the remaining bottom portion of the mtj stack is etched with a mask to electrically isolate adjacent mtjs , the m2 alignment marks 106 are rendered vulnerable to additional damage as illustrated by the shaded area 126 in fig5 . byway of example , fig6 illustrates a failure analysis image of m2 alignment copper that is roughened by exposure to ion bombardment in the mtj and strap etch processes . where an etch stop layer is used within an mtj stack layer ( e . g ., as disclosed in u . s . patent publication 2005 / 0254180 , also assigned to the assignee of the present application ), the problem could be exacerbated even further due to the additional amount of etching . because the copper in the m2 metal lines 110 is covered by the mtj stack 116 the entire time in the tj and ma etches , it is therefore not exposed to damage . on the other hand , the m2 alignment marks 106 left vulnerable to damage are subject to surface roughening as described above . this roughening of the copper surface of the alignment marks 106 in turn results in an ill - defined reflection of the laser light that is shined upon the marks in the litho stepper for subsequent mask levels . for example , when attempting to align a via for connecting the strap ( bottom ) of the mtj stack 116 to a corresponding m2 line 110 , the scattering of light from the damaged cu surface results in poor alignment and attendant yield loss . therefore , in accordance with an embodiment of the invention , there is disclosed an improved alignment mark and masking scheme for magnetic tunnel junction elements that circumvents the above described alignment problems associated with a “ single mark ” technique that utilizes a singular set of alignment marks and overlay boxes . briefly stated , an additional set of alignment marks and overlay boxes is formed in the kerf region of a wafer level . by forming two complete sets of alignment marks , and by patterning the hardmask / mtj stack open step such that only one of the two sets of marks is optically exposed , the second set of alignment marks not exposed still remains protected ( along with the lower level metal lines to which alignment is sought ). referring now to fig7 , there is shown a cross - sectional view of a portion of processing of an mram device prior to an alignment step in which a conductive hardmask is aligned to lower level conductors . for ease of illustration , like elements are designated with the same reference numerals as in earlier figures . again , in the example depicted , the lower metal level represents the m2 wiring level of an fet - based mram . however , it should be understood that although the dual alignment mark methodology presented herein is in the context of mram device processing , it is contemplated that the technique is equally applicable to other types of semiconductor structures in which alignment of opaque elements is carried out . as will be particularly noted from fig7 , in addition to a first set of alignment marks 106 a ( alignment marks 102 and overlay boxes 104 ) formed in a dielectric layer 108 , a second set of alignment marks 106 b ( having alignment marks 102 and overlay boxes 104 ) is also formed in a kerf region of dielectric layer 108 . one of the m2 metal lines 110 is also shown adjacent the second set of alignment marks 106 b . for alignment purposes , it is seen that the block mask opening 119 ( as described above ) optically exposes the first set of alignment marks 106 a , but the second set of alignment marks 106 b is still covered by the opaque mtj stack layer 116 and hardmask prior to hardmask alignment to the m2 metal lines 110 . in other words , the optically exposed set of alignment marks 106 a is used for hardmask alignment , while the second set 106 b is not . thus , following the subsequent etch processing of the mtj stack to form the tunnel junctions and strap portions of the device , the first set of alignment marks 106 a are still subject to being damaged , as shown by region 126 in fig8 . however , the second set of marks 106 b is undamaged . for example , fig9 is an analysis image of alignment mark metal that is left undisturbed through the dual alignment mark scheme of fig7 and 8 . moreover , since both the first and second sets of alignment marks are formed in the same mask level , it is still possible to effectively align with the first set of marks 106 a ( although damaged ) by aligning with the second set of marks 106 b and using a constant offset ( designed into the m2 level reticle as the offset between the first and second set of marks ). although the above described approach utilizes more real estate in the kerf regions of the metal level ( s ) where the dual alignment marks are formed , there is a significant improvement in terms of the integration capability of mram devices with respect to standard cmos processing . specifically , the presence of a second set of alignment marks that are undamaged by subsequent mram etch processes are available for downstream integration steps associated with standard cmos integration . while the invention has been described with reference to a preferred embodiment or embodiments , it will be understood by those skilled in the art that various changes may be made and equivalents may be substituted for elements thereof without departing from the scope of the invention . in addition , many modifications may be made to adapt a particular situation or material to the teachings of the invention without departing from the essential scope thereof . therefore , it is intended that the invention not be limited to the particular embodiment disclosed as the best mode contemplated for carrying out this invention , but that the invention will include all embodiments falling within the scope of the appended claims .