i personally like this for ditching comments and blank lines (but obviously this is a TMTOWTDI item):

while (my $line = <DATA>) {
    chomp $line;
    $line =~ s/\s*#.*//;
    unless $line =~ /\S/;
    ...
}
[download]

Also note that for the path creation you can use File::Path

my $dir = "$base_dir/$filepath"
do { mkpath $dir; print "Made $dir\n"; } unless -d $dir;
[download]

As for the original issue, I'm not sure where those blanks are coming from.. It doesn't seem like it's one trailing line at the end of DATA.. to debug further i would first try this and hope the answer becomes apparent:

warn "Line: ==$line==";
my ($filename, $filepath) = split '\t', $line;
warn "filename: '$filename' --- filepath: '$filepath'";
[download]