my @infiles = &GetINDirFiles($inpath);  
# instead of having an array with the outfiles use a hash for faster lookup
# also remove suffix at this stage already, no need to do it again and again in the loop
# you need to escape your suffix variable in \Q...\E for special characters such as the dot
# only remove the suffix at the end, no need for (.*)
my %outfiles = map { s/\Q$outsuffix\E$//; $_ => 1 } &GetOUTDirFiles($outpath);

my $index = 0; # index used to get string position in array
foreach my $infile (@infiles) {
		# see above re the replacement
		$infile =~ s/\Q$insuffix\E$//;      # remove suffix to do comparation # Added by me
		# instead of loop through array of outfiles do hash lookup
		push (@delindex, $index) if exists $outfiles{$infile};
		$index += 1;
}