I want to build an app in which the user will draw some shape, and then i will use the points' coordinates in this sketch to do some calculations. Is there some tool in matlab that could help me achieve this interaction?
You might want to use UIAxes for your requirements.
You can have a On/Off toggle, while the switch is on, you would like to retreive pixel coordinates of the mouse clicks in the code for further calculation and while the switch is turned off, return nothing. To acheive the same, please look into this thread.
And if you want to draw shapes in UIAxes then you might look into this thread.
For drawing freehand shapes, try looking into this thread.