My first recommendation is that you need use strict; in your code. This will REALLY help with the debugging.

Second: don't use the same name for scalars and arrays (e.g., my $scope_ct = @scope_ct;). It is too easy to make a mistake w/o realizing it.

EDIT: I made a few very minor changes based on the errors from using strict/warnings and now your script seems to work (see below). If I were you, I'd still go back and rename some variables to make your script easier to expand/maintain/troubleshoot in the future.

#!/usr/bin/env perl
use strict;
use warnings;
use bignum;

# pseudocode
#   print "Enter number of counts"
#   $ct = <>;
#   @arr = ();
#   for ($i = 0; $i < $ct; $i++) {
#       each iteration of loop calls subroutine
#       to get cell counts from user and stores in variable
#           push() variable to store in array
#       $count_i = &indiv_count()
#           push (@arr, $count_i);
#       }
#   output @arr
#       $arr_len = @arr;
#       print "The counts were:\n";
#       for ($j = 0; $j< $arr_len; $j++) {
#           print "Count number $j was arr[$j]\n";
#           }

print "Enter number of counts.\n->";

my $ct = <>;
chomp $ct;
print "\n$ct";
my @arr = ();

for ( my $i = 0 ; $i < $ct ; $i++ ) {
    my $count_i = &indiv_count();

    push( @arr, $count_i );
}

my $arr_len = @arr;

print "The counts were:\n";
for ( my $j = 0 ; $j < $arr_len ; $j++ ) {
    my $iteration = $j + 1;
    print "Count number $iteration was $arr[$j]\n";
}

sub indiv_count {
    my ($input);
    print "Enter individual count from scope.  Press Enter without inp
+ut to end list\n";
    my @scope_ct = ();
    while ( $input = <STDIN> ) {
        chomp $input;
        last if ( $input =~ /^\s*$/ );
        push( @scope_ct, $input );

    }
    my $cell_sum;
    my $scope_ct = @scope_ct;
    for ( my $i = 0 ; $i < $scope_ct ; $i++ ) {
        $cell_sum += pop(@scope_ct);
    }

    my $cell_ct = ( ( $cell_sum / $scope_ct ) / 0.0000015 );
    return $cell_ct;

}
__END__
$ ./cell_counter.pl
Enter number of counts.
->3

3Enter individual count from scope.  Press Enter without input to end 
+list
1
2
3

Enter individual count from scope.  Press Enter without input to end l
+ist
4
5
6

Enter individual count from scope.  Press Enter without input to end l
+ist
7
8
9
10

The counts were:
Count number 1 was 1333333.333333333333333333333333333333333
Count number 2 was 3333333.333333333333333333333333333333333
Count number 3 was 5666666.666666666666666666666666666666667
[download]

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