Hello, you asked the wrong question: if you split your file using "module xxx/endmodule" you end up with two empty lines.
What you really want is to grab everything between two markers to go in separates files. I underline this because the wrong question preclude you to obtain good answers.

In the case you describe you'll find very useful the flip-flop operator, a not well known operator, very useful insetad, described in the docs

#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

my @files;
my $file_index=0;

while (<DATA>) {
  if ($_ =~ /^module\s+/ .. /endmodule$/){
      $files[$file_index].=$_;
  }
  else {++$file_index;}
}
print scalar @files," elements in \@files:\n",Dumper (\@files);



__DATA__
module soc (PAD_TEST , VDIG_ON , GNDD_ON , VPP_EF , PAD_BOND_OPT );
inout  [31:0] PAD_TEST ;
input  VDIG_ON ;
input  GNDD_ON ;
inout  VPP_EF ;
inout  [5:0] PAD_BOND_OPT ;
endmodule

module analog_atop_wrapper (PAD_VDDTX , PAD_VREFADC , PAD_VSSRF ,
    DPAD_GSUB_XTAL24M , DPAD_GSUB_RX );
inout  PAD_VDDTX ;
inout  PAD_VREFADC ;
inout  PAD_VSSRF ;
inout  DPAD_GSUB_XTAL24M ;
inout  DPAD_GSUB_RX ;
endmodule

module misc_atop_wrapper (VDIG , VRTC , AVDD , EBUS , IOGND , VDIG_ON 
+);
inout  VDIG ;
inout  VRTC ;
inout  AVDD ;
inout  EBUS ;
inout  IOGND ;
input  VDIG_ON ;
endmodule
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HtH
L*