Depending on how they are attached, I've actually snapped them apart. I then use my wire cutters to trim the pieces down. I haven't had any problems with bending the die. But sometimes they are attached together in such a compact cluster that it is hard to get them to break apart.
The wire cutters I usually use are the pair I bought for working with florals. But I also have ones for jewelry making, which are smaller and should fit in the tight spaces.