Replacing WordPress core files

Hi,
My webmaster told me that i have malicious files in different folders of my WordPress. For security reason the site is not accessible. Now my database is fine but was suggested by host that I should either manually delete all malicious files Or rebuild the site from scratch. Can someone please suggest me if its possible if i only replace those folders in core WordPress which contain malicious files will that be sufficient and doable? OR Please suggest me some way to fix without rebuilding it from scratch. I don’t want to use plugins rather want to do it manually.