#!/usr/bin/perl -w

# read data
my @multi_array; push @multi_array, [split(',', $_)] for <DATA>;
#@multi_array = map {s/\s//} @multi_array;

# add counter column
my $i = 0; (chomp $_->[1],$_->[2] = sprintf ("%d",$i++)) for @multi_array;
#or
push @{ $multi_array[$_] }, $_ for 0 .. $#multi_array;

# modify columns
($_->[0] *= 1.0, $_->[1] /= 1.0) for @multi_array;

# screen output	
print join(",", map { sprintf "%e", $_ } @{$_}),"\n" for @multi_array;

__DATA__
0.00000000e+00, 2.41644835e+00
1.20048018e-04, 2.38938189e+00
2.40096037e-04, 2.36473989e+00