As long as the application launches using specfic credentials (such as a service, or task) you should be able to modify the NTFS ACLs on the system to allow only that credential and not other users. Would need more info on your specific application to comment further.
Here's what to do to get your app to run as a service (this was taken from the technet forums)....
At the time of this posting, there is no Windows Server 2008 Resource Kit Tools, so get the "srvany.exe " from the "Windows Server 2003 Resource Kit Tools " and copy it to a suitable location on your Win2008 server (e.g. C:\Windows\System32\ ).
Use "sc " to create a new service that launches "srvany " (e.g. sc create MyService binPath= C:\Windows\System32\srvany.exe DisplayName= "My Custom Service" )
Using RegEdit : create a "Parameters " key for your service (e.g. HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\MyService\Paramaters\ )
Using RegEdit : within the newly created "Parameters " key , create a string value called "Application " and enter the full path to the application you are wanting to run as a service. (No quotes required.)
And that should do it.
Note : some applications store their settings in a user hive, not under HKEY_LOCAL_MACHINE, so you will need to run the application to configure it, and then configure the service to run as that user.