My thoughts upon reading this (which I hope would prove helpful) were :

1. Use File::Find to generate a list of files (also potentially at this point exiting or asking for processing options for duplicate file names)
2. Use the -d dirname test, mkdir() and File::Spec to create subdirectories that may be needed
3. Use File::Copy's copy() function for the final movement

At least, that's the process I would likely procede with (assuming a better solution were not proposed).

HTH.