If you have zipped up a directory from a Mac OSX machine and unzipped it on a linux box, chances are you have heaps of hidden files that look like ._myfile and ._mydirectory – these are files that OSX uses to keep track of additional information about your files.
To remove these, do the following at the command line:
find . -name "._*" -print0 | xargs -0 rm -rf
That will remove all the files and you will have a clean linux hierarchy!