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I'm activating the built in ArcGIS measure tool using the following code:

ControlsMapMeasureTool measureTool = new ControlsMapMeasureToolClass();

// set current tool to be measure tool
_axMapControl.CurrentTool = measureControl as ITool;

// deactivate measure tool
_axMapControl.CurrentTool = null;

Whenever I deactivate the tool the window opened by the tool is not closed. How can I cause it to close?

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As far as I can tell there is no interface for the measure tool dialog and thus no way to close it using ArcObjects. I think you'll have to use the Windows API functions FindWindowEx to find the child window handle corresponding to the measure tool dialog, and DestroyWindow to close it and release its memory resources.

See for C# function definitions for these:

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