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What using a custom filter does is not record the method or any sub-methods that method makes in the results. However the line that called MsgBox still took time and this is the time that you are seeing.
In order for you remove that entirely you would need to exclude the method that called MsgBox - it would still get included in the application run-time time but wouldn't be included in the All methods view or anything else.
If you look at the All methods view you'll see that MsgBox isn't there so your filter is working.
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In custom filter(Do not profile .NET methods that start with) following are the strings that I have entered:-
But still message boxes are being profiled by Ants Profiler.
I want to exclude msgbox because the time that the message box is shown in the screen before the user clicks on any button is included in the result.