#!/usr/bin/perl

use strict;
use warnings;

while (<DATA>) {
    s/(?:^.*?>>\h*|\G(?!^))\K./\\$&/g;
    print;
}

__DATA__
Aenean placerat >> /example/alpha.txt
est et rutrum ultrices >> /example/beta.txt
dolor nibh ultricies nulla >> /example/gamma delta.txt