You could shift those parts from the current loop towards the outer loop that do not depend on the variables of the current loop (= are constant in that loop). This avoids unnecessary re-computation and might slightly improve performance.

use warnings;
use Win32::OLE;
use Win32::OLE qw(in with);
use Win32::OLE::Const "Microsoft Excel"

my $yes = "yes";  #-- moved: constant for both loops
 
for ($begincol;$begincol<$totcol;$begincol++) {
    my $app = $sheet2->Cells(3,$begincol)->{'Text'}; #-- moved: consta
+nt for next loop

    for ($beginrow;$beginrow<$maxrows;$beginrow++) {
        my $cap = $Sheet2->Cells($beginrow,5)->{'Text'};
        #-- moved out of inner loop:  my $app = $sheet2->Cells(3,$begi
+ncol)->{'Text'};
        #-- moved out of both loops:  my $yes = "yes";
        if (index($app, $cap) != -1) {
            $Sheet->Cells($beginrow,$begincol)->{Value} = $asis;
        }
    }
$beginrow = 7;
}
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