she bought a knife from the shop with ---- to peel an apple.

因为with是个介词,后面一定要跟which,在这里是不能用that来代替which的~中文意思：她在店里买了一把刀,用它来削苹果。（peel an apple with a knife）中文意思的用就对应着with,它就对应着which。