Bad backlinks for a website can be removed by contacting the webmasters individually. Google disavow tool will help to list the webpage that contain bad backlinks for your website, and you need to contact them individually to get the links removed.
You can use Disavow tool to remove bad links. But one thing which you need to keep in your mind that you can use this tool if you got any manual action warning from google. If your website ranking fall considerably only then you can consider this option for your website.
You can check which low quality pages on your website are linked by bad backlinks and get rid of the pages .i.e. 404/410, instead of the links. In addition to getting rid of the page, you should also disavow these bad backlinks.
Use Google Webmaster Tools to get a list of your backlinks and check the most recent first. If you believe that your site or individual pages are being harmed by links over which you have no control, you should ask the webmaster of the other site to remove them. If this fails, then you can use the Disavow tool to flag them so that Google ignores them.