use the RemoveDirectory method of the WebRequest methods.
The sample snippet does what you need.
FtpWebRequest myFtpWebRequest = null;
myFtpWebRequest = (FtpWebRequest)FtpWebRequest.Create(new Uri(folderPath));
myFtpWebRequest.Method = WebRequestMethods.Ftp.RemoveDirectory;
myFtpWebRequest.UseBinary = true;
myFtpWebRequest.Credentials = new NetworkCredential(userid, password);
FtpWebResponse response = (FtpWebResponse)myFtpWebRequest.GetResponse();
....
Needless to say, you need to provide the stuff marked.
Note that this method is only available in .Net framework versions 2.0 and above. The documentation can be found http://msdn.microsoft.com/en-us/library/system.net.webrequestmethods.ftp.removedirectory(VS.80).aspx.