This logic looks odd because if $FileExt is '.pdf' then it's length (4) will always be greater than 3

if ($FileExt eq ".pdf"){ 
  if  (length($FileExt) > 3){
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You haven't shown the whole code but it may help you to reduce the levels of ifs with some early next statements like this ;

while (my $filename = readdir(DIR)){

  next unless (-f $filename);
  next if ($filename eq $SumRptNam);
  
  if ($filename =~ /\.(pdf|xlsx)$/){
    my $FileExt = $1;
    if ($FileExt eq 'pdf'){
      # do X to pdf
    } 
    if ($FileExt eq 'xlsx'){
      # do Y to xlxs
    } 
    # do Z to both
  }
}
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edit : quotes removed from '$SumRptNam'

poj