How do I prevent OS X from making ".filename" files?
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