A method and system for customizing a gaming machine by transferring software files from a download server to a gaming machine. The download server may store software files in three-tier hierarchical structure and execute program logic to determine which software files need to be transmitted to the gaming machine to customize the gaming machine. The method may include (i) determining a download signature for software files that correspond to the gaming machine and that are stored at the download server, (ii) determining a machine signature for software files stored at the gaming machine, (iii) comparing the download signature to the machine signature, and (iv) allowing the gaming machine to carry out gaming functions if the signatures match, or (v) if the signatures do not match, updating the gaming machine with gaming machine software files and, thereafter, allowing the gaming machine to carry out gaming functions.