How do I prevent OS X from making ".filename" files? I'm not sure of the consistency but sometimes OS X makes hidden .filename files where filename is a name of another file in the same directory. I want to know how to disable this since USBs I insert and copy / move files to / from keep having this and it's annoying to have to delete them every time I plug the USB onto a non-Mac computer.
What format is the volume in? If you mean the AppleDouble files that start with ._, they are not normally created on HFS volumes. They are used to store metadata like extended attributes, ACLs, and resource forks on non-HFS volumes.

You can delete the ._ files with find:

find /Volumes/volume -name ._\* -delete


If the volume is in an HFS format, you can use dot_clean to remove the ._ files after merging the metadata stored in them with the metadata stored in native formats:

dot_clean /Volumes/volume