#!/bin/bash

ls -1 Modern* | while read FILE
do
        echo `cat /media/Data/Fix/file_list.txt |grep "$FILE"`
        #echo `sed -i 's/$FILE//g' $dir`
done

Output:

/Share/TV/Modern Marvels/Season 12/Heroes - Season 2 - DVD 1/VIDEO_TS/ADV_OBJ/VIDEO_TS/functions/engines/html/html/Modern Marvels - Horsepower.mpg

Desired Output:

/Share/TV/Modern Marvels/Season 12/Heroes - Season 2 - DVD 1/VIDEO_TS/ADV_OBJ/VIDEO_TS/functions/engines/html/html/