There are ways to force this, but it's a bad idea - you will probably cause more damage by forcing the handle to close prematurely than you will save by lettign the user know and close the application manually.
But ... you say "its saying its open in my program" which implies you have opened the file - which makes sense since you are scanning it - and have not yet closed and disposed your stream with switch you are reading the file. In which case, the comment I made in the first paragraph comes into effect - you will be closing somthing your own application is using, and there is a very good chance that your app will crash as a result of your forcing the delete.
Instead, check your code, and make sure that all streams, file handles or whatever you are using to access files are correctly Disposed before you try to delete them.
Dim isSuspect As Boolean = False
Using fs As New FileStream(path, FileAccess.Read)
isSuspect = ScanMyFile(fs)
End Using
If isSuspect Then
...
End If