Remove timthumb.php from my custom theme

Just delete your timthumb.php file.

If your site thumbnails use timthumb then the code might look like this

<img src="https://wordpress.stackexchange.com/questions/80287/<?php bloginfo("template_directory'); ?>/xxxxx/timthumb.php?src=<?php echo "original image url" ?>&h=150&w=150&zc=1" /> 

Just replace those instances with code like this

   the_post_thumbnail('thumbnail', array('class' => 'thubnail'));