If you mean that you have many structure files for the same protein but with different ligands you can automatically align them all based on just the target site CA atoms (i.e. defined as those close to one of the ligands) using the Job/Cocrystal superposition application in MIFit8 http://code.google.com/p/mifit/ See tutorial lesson 15. One of the outputs is a file containing all of the aligned ligands.
It is also possible to perform bulk import of prealigned PDB files placed in the same directory with the normal File/Open Models... command but holding down the shift button and selecting the many structure files with the mouse. Different models will be displayed in different colors. For medically interesting proteins it is increasingly the case that there are dozens of cocrystals in the PDB and it becomes tedious to understand how they relate to each other without an alignment tool that can automatically run over the whole set.
