How do I remove the subdirectories from the directory struture using Perl?

You have to iterate over the directories.

A possible solution:

use File::Basename;

sub ProcessDirectory{
    my ($workdir) = shift;
    print "Processing '$workdir'\n";
    my $mask = $workdir . '/*';
    # glob: Return list of filename expansions for search mask
    # grep -d: Extract directories from list
    my @dirs = grep { -d } glob $mask;
    foreach $d (@dirs)
    {
        # Process sub directories
        ProcessDirectory($d);
        my $dirname = basename($d);
        if ($dirname =~ /^temp*/)
        {
            print " Removing $d\n";
            my $filemask = $d . '/*';
            # Delete all files in directory and then the directory
            #unlink glob $filemask;
            #rmdir $d;
        }
    }
}

ProcessDirectory('/home/rperiasa/output');

Note that I have commented the remove operation so that you can check the operation first.