The chomp suggestions above should resolve your immediate issues.

I offer the following style suggestions, as an alternative I consider superior:

1. For more idomatic perl, consider using the following alternative way to write your "for $j" and "for $i" loops.

for my $letter("A".."B"){
   for my $num(1..5){
           print qq[$letter$num ];
   }
}
# Prints the sequence --
#  A1 A2 A3 A4 A5 B1 B2 B3 B4 B5
[download]

2. Instead of writing code to do your search, you could make Excel do the work for you, by using the Find method of the Range object.

Details at MSDN.
(FYI: I had previously posted this in response to Simple Question - Simple Answer, I hope)