To manually remove the links:
1. Get the whole list of your site backlinks. For that, go to Google Webmaster Tools. On the website Dashboard, go to
Search Traffic => Links to Your Site => Who links the most => More. Click Download more sample links. All of these services provide you with different backlinks so you need to combine the reports and remove duplicate URLs if there are any.
2. Evaluate each of your backlinks and find those which can be potentially harmful. Doing it manually can take a lot of time, if there are many backlinks to review. If you're looking for free services, try Netpeak Checker which can evaluate backlinks in bulk by multiple parameters. WebMeUp does that too, BTW.
3. Contact webmasters of each potentially harmful website asking them to remove links to your website.
4. Straight from Google guidelines
: If you?ve done as much work as you can to remove spammy or low-quality links from the web, and are unable to make further progress on getting the links taken down, you can disavow the remaining links. In other words, you can ask Google not to take certain links into account when assessing your site.
5. For that, create a file containing only the links you want to disavow, and upload this to Google at
https://www.google.com/webmasters/tools/disavow-links-main. Note that your file should be in .txt format and contain only the links you want to disavow ? one link per line.
Do NOT!!! submit a file with all links to your website.
If you want Google to ignore all links from an entire domain, add the line "domain:example.com". It's also recommended that your text file includes additional info about these links, like comments about when you contacted the webmaster and what was the result. Start comment lines with the "#" character.
5. Submit reconsideration request to Google if your website got penalized for unnatural link building.
Check out additional info at
https://support.google.com/webmasters/answer/2648487?hl=en.
