You can populate your arrays like so:

open (FILE1, $file1);
open (FILE2, $file2);
@filearray1=<FILE1>;
@filearray2=<FILE2>;
[download]

Then you'll want two arrays containing the first column values of each filearray:

for(@filearray1){
  ($col1)=split;
  push@colarray1,$col1;
}
for(@filearray2){
  ($col1)=split;
  push@colarray2,$col1;
}
[download]

Then you can manipulate / compare these two arrays as you see fit.
Jason