The Application Virtualization cache can cause a number of issues with conflicts, size limitations and more. Most of these issues are simple to solve by simply clearing the cache and it should be one of the first steps you do when troubleshooting Application Virtualization.
From the registry, drill down to HKLM\SOFTWARE\Microsoft\SoftGrig\4.5\AppFS\ and change the State key to “0” and reboot the machine.
There are two command line options as well, one to remove all applications:
sftmime.exe remove obj:app /global /complete
And one to remove a specific application:
sftmime.exe remove app:”applicationName” /complete
If you don’t know the name of the application you want to remove you can get a list of them with this command:
sftmime query obj:app /short