Make files invisible:

SetFile file -a V

SetFile can change a lot of other file attributes and metadata, as well.

SetFile is not a OS X native command it comes bundled with DevTools/Xcode.

If you don't have Xcode and don't want to download about 6 GB, you can use

sudo chflags hidden|nohidden <file/folder>

chflags is a BSD command and it also has a Man Page just enter this in Terminal

man chflags

for those who don't like to enter commands self and just would like to know what there stands in the man. Here you have: