Hi,
It is a little more complicated than just running an upgrade file. If you are going to upgrade from CM 3.0 to CM 3.1, you will need to have CCO access and a contract that allows you to download the software. If you have the proper access to get the files, the FIRST thing that you will need to do is upgrade the operating system. There is a file in the cryptographic software section of the CallManager 3.1 area called win-OS-Upgrade.3-1-2spA.exe. (http://www.cisco.com/cgi-bin/tablebuild.pl/cmva-3des). This will give you the proper service pack and hotfixes. You may also need the BIOS upgrade, depending on your platform. Once you have upgraded the OS, you can then download and install the upgrade. Here is the URL for the upgrades. http://www.cisco.com/cgi-bin/tablebuild.pl/callmgr-31
Make sure that you download and READ the release notes prior to performing the upgrades!
Scott