a method of inhibiting pit occurrence on a semiconductor substrate during manufacture of a semiconductor device includes forming an isolation using a shallow trench isolation method in a semiconductor substrate , forming an insulation layer on an entire surface of the semiconductor substrate having the isolation , implanting ions into the semiconductor substrate using the insulation layer as a buffer layer , annealing the semiconductor substrate using a rapid thermal annealing process , forming a photoresist layer on the insulation layer and then forming an opening in the photoresist layer to expose an underlayer thereof , forming an align key by etching the underlayer at the opening , and removing the photoresist layer and the insulation layer . alternatively , the thickness of the insulation layer may be reduced to prevent the occurrence of pits on active areas of the semiconductor substrate .