I have manage to improve the program and reduce the weird loopings based on your advice. I am kind of stuck at the if condition part, in which I am unsure if it is the correct way to search for the data. I hope I am in the correct direction.

    
while (<LIBRARYDATA>)
 {
    
    #add the name, mass, rt(time) and type to an array
    chomp $_;
    my @columns = split (/\t/, $_);    
    
    my $keyname = $columns[0]; 
    my $keymass = $columns[1];
    my $keytime = $columns[2];
    my $keytype = $columns[3];
    
   
    my $key = "$keymass"."\t"."$keytime"."\t"."$keyname"."\t"."$keytyp
+e"."\n";

    # Mass (to allow range for user to search based on tolerance they 
+input)
    $masst1 = $keymass + $masstoleranceinput;  
    $masst2 =  $keymass - $masstoleranceinput;  
        
  for ($keymass)
   {     
    for ($keytime)
    {
     if (defined ($keytime) && defined ($rtinput)) #skip those with bl
+ank cells at "Time" column
      {
       #allow user to choose time range based on tolerance they set
       $rt1 =  $keytime + $rttoleranceinput;         
       $rt2 =  $keytime - $rttoleranceinput; 
       
        #match according to mass and time against library
        if (( $masst2 <= $massinput && $massinput <= $masst1 ) && ( $r
+t2 <= $rtinput && $rtinput <= $rt1 ))
        {
         print OUT1 "$massinput\t$rtinput\t\t$key";
        }
       }
        else #for those cells at "Time" column that is left blank, go 
+to this loop where only mass is being matched
        {
           #match against mass only
       if (( $masst2 <= $massinput && $massinput <= $masst1 ))
           {
            print OUT1 "$massinput\t$rtinput\t\t$key";
           }        

        }
      }
    }
 }
[download]

rtinput and massinput is key in by user, in which sometimes the rtinput will be leave blank. $masstoleranceinput and $rttoleranceinput is also by user input.

LIBRARYDATA refer to the data that I want to match the user inputs with. Some values under "Time" will be blank.

_LIBRARYDATA_
Name   Mass     Time   Type
John   223.41   1.20   Boy  
Betty  111.23          Girl
Ken    100.25   0.56   Boy
.
.
.

_INPUTDATA_
e.g. 
Mass     Time 
100.20   0.55
150.34   0.23
223.45   1.22
223.44
[download]

The problem I have here is that there will be error once it pass through the first if loop where the error stated that it is unable to do calculation if the value is left blank. Since I have add in that if the values is defined, then continue, otherwise, skip to the next if condition which is just to compare the mass alone.

So did I miss out something which cause the error and prevent those (with the value of "Time" left blank) from printing out?

...

:) I'm sorry to say I don't think you have done enough ( How (Not) To Ask A Question )

What you posted looks nothing like the program I wrote that I wanted you to use and continue and finish( Re: Search based on user input and return values (more subs) )

While the number of loops has decreased, you still got for($foo){ .. for($bar){ .. which does nothing, it only takes up indentation space

And you still don't have any subs ... still incomplete code that won't run as posted

I had a similar interaction with james28909 in directories and sub directories and copying or moving hundereds or thousands of files :)

I also had a similar interaction with hellohello1 in Re: How to store the output from foreach loop into variable/array without printing? where you played along after a while, but ultimately never used these ideas again

You don't have to take my advice and do what I say :)

Its ok if you have a subroutine allergy, you can live with it, its not fatal :)

But I like to keep my distance :)

Good luck

Hi, I'm sorry. I'll try again! I'm not that allergic to subroutines, I am still working on it and trying to learn how to sub, but for my previous question, I was trying to ask if I am using "defined" the correct way to ensure that the blank values can be skipped. Thanks for the first link to the thread. Will read up and see how it goes. My apologies for causing you some annoyance!