Fat32 has no NTFS style security features. If you were on a Domain, I suppose you could use policy to deny access to certain partitions on a box based on the user. I am guessing this is a standalone machine though, so any policy limits you place on the box will stand for all users, including yourself. That's not what you want.
Unless you have a good reason to be using FAT32 (WIN 98 dual boot for example), I would just format the other partitions as NTFS and then you can assign permissions to the files and folders as you please. You can do this without losing any data.
Right click My Computer and select "Manage"
Expand the tree and select Disk Management.
In the Left pane you will see your disk(s) and the partitions.
Right click a FAT32 partition, and select format. Choose NTFS as your option.
The system may or may not require you to re-boot. I can't remember.
Good luck