The new application model in System Center Configuration Manager 2012 is pretty excellent, and allows you to do some innovative software deployments. But, like any new thing, the UI takes a bit of getting used to. In this case, there’s no delete/erase button for Applications which you no longer require.
This is because an Application in SCCM 2012 is quite distinct from a traditional Package in SCCM 2007, and is likely to have hooks into all sorts of places. You can still remove Applications from SCCM 2012, but there’s a process to follow:
1 – Delete any active Deployments
2 – Delete all the Deployment Types
3 – Right-click the Application and select “Retire”
4 - Right-click the Application and select “Revision History”
5 - Starting at the bottom of the list, highlight each revision and click Delete
6 – When you delete the last revision you’ll get a warning that proceeding will remove the application permanently. Click Yes and you’re done