Some significant revisions of Merge can co-exist. For example, Merge 2007 (or later) can be installed on a machine at the same time as Merge v6.5. If you are installing a relatively minor update (for example, if you install 2007.3241 on a machine with 2007.3225 already installed), the recommended Merge setup will automatically uninstall the existing version of Merge if it cannot co-exist with the new version.
If you are not using the recommended setup, you should manually uninstall Merge using Add/Remove Programs (or in Vista, Programs and Features) in Control Panel before installing a newer version.