foreach my $interval (<INTERVAL>){
       
     my @find_interval = split(/\t/, $interval);
     my $start = $find_interval[1]; 
     my $end = $find_interval[2];
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Be aware that this loop will read the entire file accessed by the  INTERVAL filehandle into memory at once as an array, each line of the file being an array element. The
    while( <INTERVAL> ) { ... }
loop reads and processes a line at a time: much more scalable, insignificant speed difference, if any.

my @find_interval = split(/\t/, $interval);

I would split directly into the named variables you will be using, and split on  '\s' (whitespace) to avoid having a newline stuck to the end of the third field element:
    my (undef, $start, $end) = split '\s', $_;

It would accomplish the same thing, yes. It may be more readable to use the former syntax if the array being split isn't huge however. So you are masking regions of the genome I take it?

Yes indeed, just one chromosome for this program. The intervals are generally small but numerous in number since small interspersed sequences have been filtered out. 124467 intervals actually. It appears it will take a bit of time to go through all of them but I can't even imagine doing it the way I first proposed. Thank you for the help!

The text file being read has 3 columns, the first of which is non-numeric. If I specify the variables with foreach ... would that accomplish the same thing?

Sorry, my mistake. However, I'd stick with while rather than foreach. There is simply no benefit to filling memory with an entire file (however big) if you can only use 1 line at a time:

while( <INTERVAL> ) {
     ## ignore the first field on each line
     my( undef, $start, $end ) = split "\t", $_;
...
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