I wish to modify my current linking structure i.e. changing file names, how much will it affect my SERP ?
if you use 301 for clocking than it's black hat but if you use for your old url's to redirect on newer than it's recommended and white hat.
Read this, if you're doing 301 redirect, this will let you know how you can do 301 without hurting your site's performance in Google search.
It depends on how dramatic the changes are, even if you do a 301 from the old URLs, a sitewide change of hundreds or thusands URLs will make you site suffer for a few weeks, often months. In general I'd never recommend any major URL changes in existing projects, if they aren't absolutely neccessary.
If you are changing the URLs of pages in your site, then that will affect SERPs a lot. But if you properly 301 redirect the pages, you will get back your ranking in some time.
I created a excluded urls in robots.txt and sent an url removal request from webmasters tool and within 3 hours all were disappeared from index thanks for help.