Your code can be optimized a lot. Here is some proposal but I cannot test it as I do not have your directories at hand. I added comments to explain what I am doing so I hope it helps:

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

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 comp
+aration # Added by me
        # instead of loop through array of outfiles do hash lookup
        push (@delindex, $index) if exists $outfiles{$infile};
        $index += 1;
}
[download]

UPDATE: Forget my code above. You can write this as:

my %outfiles = map { /(.*)\Q$outsuffix\E$/; $1 => 1 } &GetOUTDirFiles(
+$outpath);
my @infiles = grep { /(.*)\Q$insuffix\E$/; not exists $outfiles{$1} } 
+&GetINDirFiles($inpath);  
print "@infiles\n";
[download]

and it should be fast.

UPDATE 2: Here is the full story.

use strict;
use warnings;

sub GetINDirFiles {
        my ($path) = @_;
        opendir my $dir, $path or die $!;
        return grep {!/\_ACK_/} readdir $dir;
}

sub GetOUTDirFiles {
        my ($path) = @_;
        opendir my $dir, $path or die $!;
        return grep {/\_ACK.xml$/} readdir $dir;
}

# Main
my $inpath = "./IN";      
my $outpath = "./OUT";
my $outsuffix = "_ACK.xml";
my $insuffix = ".xml";     
my $timethreshold = 900;       # set time threshold in seconds (900 se
+conds equal 15 minutes)

my %outfiles = map { /(.*)\Q$outsuffix\E$/; $1 => 1 } &GetOUTDirFiles(
+$outpath);
my @infiles = grep { /(.*)\Q$insuffix\E$/; $1 and not exists $outfiles
+{$1} } &GetINDirFiles($inpath);  

my $currenttime = time;        # get current time from system (epoch t
+ime)
@infiles = grep { -f "$inpath/$_" and ( $currenttime - (stat "$inpath/
+$_" )[9] ) > $timethreshold } @infiles;

# now you have all input files w/o corresponding output file that are 
+older than 15 minutes
for (@infiles) {
        print "File $_ in $inpath directory was created ". ( $currentt
+ime - (stat "$inpath/$_" )[9] )/60.0 ."minutes ago.\n";
        # put your action here
}
[download]

My requirement is to check if a new file comes into IN folder, with a maximum delay of 15 minute same file with _ACK.xml is present in the OUT Directory or not?

for example a01.xml comes in the folder IN, this will be processed by the application and sent it to OUT folder after processing (maximum time of processing is 15 minute) as a01_ACK.xml.

Content is not important in this case. in windows i can use WMI to to check if new file is created in IN directory (instance created) and then check for the same in OUT folder but in UNIX i can not get such trigger so i had to choose the way of comparing files but i am not much into UNIX so cant think other than this.

-KAKA-

Does this do what you want?:

#! /usr/bin/perl
use strict;
use Math::BigFloat;
Math::BigFloat->precision(0);

sub GetINDirFiles {
        my @files;
        my ($path) = $_[0];

        opendir (my $directory, $path) or die $!;
        while(readdir $directory) 
            {
                push (@files, $_) unless (($_ =~ m/_ACK_/) || ($_ =~ m
+/^\./));
              
            }
         closedir $directory;
        return(@files);
}

sub GetOUTDirFiles {
       my @files;
       my ($path) = $_[0];

        opendir (my $directory, $path) or die $!;
        while(readdir $directory) 
            {
                unless ($_ =~ m/^\./)
                    {
                         push (@files, $_) if $_ =~ m/_ACK.xml/;
                    }
             }
         closedir $directory;
        return(@files);
}

# Main
my @range;
my $inpath = "./IN/";
my $outpath = "./INACK/";
my $outsuffix = "_ACK.xml";
my $insuffix = ".xml";                #    Added by me 
my $timethreshold = 900;       # set time threshold in seconds (900 se
+conds equal 15 minutes)
my @delindex;
my @infiles = &GetINDirFiles($inpath);
my @outfiles = &GetOUTDirFiles($outpath);
my $index = 0; # index used to get string position in array
my $count = @infiles;

for (my $x = 0; $x < $count; $x+= 1)
    {
        my $name = $infiles[$x];
        $name =~ s/$insuffix//;
        
        for (@outfiles)
            {
                if ($_ =~ m/$name/)
                    {    
                        push (@range, $x) 
                    }
            } 
    }
my $rangeCount = @range;
for (my $x = 0; $x < $count; $x+= 1)
    { 
        splice(@infiles, $range[$x], 1);
    }

  # remove strings 
my $currenttime = time;      

 # get current time from system (epoch time)
foreach my $file (@infiles) 
    {
         my $fileForTime = "$inpath"."$file";

         my $mtime = ( stat $fileForTime )[9];
         my $diff = ($currenttime - $mtime);
             # ignore directories   # INSERT SUFFIX AGAIN ($insuffix)
             # get mtime from file (epoch time)   # INSERT SUFFIX AGAI
+N ($insuffix)     
          
        if ($diff > $timethreshold) 
            {  
               print "\n - file " . $file . " in " . $inpath . " direc
+tory was created at more than "  . Math::BigFloat->new($diff / 60) . 
+" minutes.";    # INSERT SUFFIX AGAIN ($insuffix)
               
               # PUT THE ACTION THAT YOU WANT DO HERE!!!
              } 
    }
[download]

NOTE: Change the pathnames!

In that case a simpler more direct approach might work for you

#!perl 
use strict;

my $inpath  = "/AAA/BBB/CCC/IN";
my $outpath = "/AAA/BBB/CCC/OUT";

# check inpath files less than 60 mins 
# and more than 15 mins old
my $min_age = 0.25/24; # 15 mins in days
my $max_age = 1.00/24; # 1 hour in days

my $count =0;
my $ignore=0;
print "Scanning in dir $inpath .. \n";

opendir DIR, $inpath or die $!;
for (readdir DIR){
  # skip if not a file
  next unless (-f "$inpath/$_"); 
  
  # filter on age
  my $age = -M "$inpath/$_";
  if ( ($age > $min_age) 
    && ($age < $max_age) 
    && ( !/_ACK_/ ) ){
  
    # build outfile name
    (my $outfile = $_) =~ s/(\.xml)$/_ACK$1/;
    
    # check outfile exists
    if (-e "$outpath/$outfile"){
      print "$_ => $outfile exists\n";
    } else {
      print "$_ => $outfile does not exist\n";
    }
    
    ++$count;
  } else {
    ++$ignore;
  }
}    
closedir DIR;
print "$count files checked - $ignore files ignored\n";
[download]

poj

but in UNIX i can not get such trigger so i had to choose the way of comparing files but i am not much into UNIX so cant think other than this.

Real "UNIX" ? If not you can use Linux::Inotify2