Carboxyl methyltransferase with activity toward prenyl lipids. In vitro, displays activity toward N-acetyl-S-farnesyl-L-cysteine (AFC) and S-farnesylthioacetic acid (FTA), an analog of AFC. [protein]-C-terminal S-[(2E,6E)-farnesyl]-L-cysteine + S-adenosyl-L-methionine = [protein]-C-terminal S-[(2E,6E)-farnesyl]-L-cysteine methyl ester + S-adenosyl-L-homocysteine Belongs to the class VI-like SAM-binding methyltransferase superfamily. Isoprenylcysteine carboxyl methyltransferase family.