Follow the following steps :
NOTE : origin here refers to your remote project location.
Step 1 : From command line navigate to project directory where your working
Step 2 : In command line run the following commands
git pull origin master /* Just to make sure you will get all the latest files from remote repository where you have hosted your project */
git rm * /* To remove all the files from you current directory */
OR
git rm file1.txt file2.txt /* to remote specific files */
git add . /* Add the deleted files for staging */
git commit -m "Removed obsolate files" /* Commit the deleted files into your local repository */
git push origin master /* Now push to the remote repository all the changes that you have done, all the deleted files will be now removed from remote repository */
Step 3 : Now you can start working with your fresh files