Add the files you want to hide to a file named .hidden with 1 file per line inside the directory those files are. Somehing like ls {files} >.hidden will work to quickly do this.
You can hide files looking from Windows with C:\>attrib +h D:\*.hidden /S (this will hide the .hidden file from the previous method). The directory I assumed D:.
You can hide these files from ls on Linux by adding this into your ~./bashrc:
ls () {
if [ -f .hidden ]; then
declare GLOBIGNORE="$GLOBIGNORE:.*:$(tr '\n' ':' < .hidden)"
ls "$@"
fi
}
This will hide the files when using ls and ls only. It also assumes you do not already have an alias for ls. ls -l will still show them but that is just another alias.
The last command I found on superuser. Please upvote that answer ;)