if you mean formatting a floppy, yes you can. Just put any DD floppy and choose 720kB in format options, then format the disk and transfer your files. You'll need CrossDOS (part of AmigaOS 3) or MSD95 on the amiga side to read such a disk.
If you mean formatting a harddrive, you can do it too. You need to have an empty (a PC drive with partitions empty/erased won't do!!!) harddisk and you can prepare&mount it under newer revisions of WinUAE, or if you don't have an empty drive, you may do one by preparing it under a real amiga, and then reconnect it to PC.