There are two classes which will be of great value to you for FTP. First, FtpWebRequest and second, FtpWebResponse. As for writing a windows service: this, and this should be helpful as well.
An example lifted from MSDN to delete a file:
public static bool DeleteFileOnServer(Uri serverUri)
{
    // The serverUri parameter should use the ftp:// scheme.
    // It contains the name of the server file that is to be deleted.
    // Example: ftp://contoso.com/someFile.txt.
    // 
    if (serverUri.Scheme != Uri.UriSchemeFtp)
    {
        return false;
    }
    // Get the object used to communicate with the server.
    FtpWebRequest request = (FtpWebRequest)WebRequest.Create(serverUri);
    request.Method = WebRequestMethods.Ftp.DeleteFile;
    FtpWebResponse response = (FtpWebResponse) request.GetResponse();
    Console.WriteLine("Delete status: {0}",response.StatusDescription);  
    response.Close();
    return true;
}
With a little bit of work you should be able to modify that to do every thing you need in terms of FTP Access.