remove_filter( 'the_content', 'wpautop' ); only for certain post types

functions.php

//decide when you want to apply the auto paragraph

add_filter('the_content','my_custom_formatting');

function my_custom_formatting($content){
if(get_post_type()=='my_custom_post') //if it does not work, you may want to pass the current post object to get_post_type
    return $content;//no autop
else
 return wpautop($content);
}