there are two 3shape folders on the c: drive. in the one folder you will see all your scanned data, in the other you will see the program libraries.
if i recall correctly, your custom library should be under the 3shape control panel\(theres a bunch of folders here) with one of them called libraries, with two folders in it named custom and 3shape standard. custom will have more subfolders for scanned waxup patterns, but one called top cap libraries, in it is your stuff divided into the names of the various systems you made stuff for.
but its late and i am very drunk and i am not near my computer.