readdir reads the directory listing. It does not supply the full path name. When you return a call to print_rec($_) you neither change the current working directory or supply the full path to the directory name being passed in $_.

Assuming you run the program from your current working directory, your recursive calls attempt to open directories listed one directory below the directory you are calling the routine from, but in the directory you are calling it from instead of from the one below.

sub print_rec {
    my $path = shift;
    opendir DIR, $path;
    while( readdir(DIR) )
    {
        if(!/\.|\.\./ && -d $_)
        {
            print "$_ is a directory\n";
            return print_rec($path.'\'.$_);            
        }
        elsif (!-d) { print "$_ \n"; }
    }
}
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