web-server hacked , file url in broswer that doesn't exist in winscp

I have one of my site hacked (added file/pages) there is also a google verification .html that i can access through url ( domain/verification_file.html) but it doesn't exist in htdocs when i search through putty ssh or winscp, how is this happened?A sitemap.xml created with urls on site that (domain/http://ift.tt/1Mu8L0w ) but the folders doesn't exist in htdocs