<p>I want to know how to make a mold of a 3D design in .stl format.</p>

<p>Suppose I have a 3D partin .stl format (for e.g. a cylinder) and I want to make/design a mold for this object (i.e. the structure through which I could make the cylinder). Is there any way to do so? Are there any tools to do so?</p>

<p>My requirement is as follows: I have an .stl file of a design and need to develop the CAD files for its mold. I will then need to 3D print these molds. I would require to add a hole to pour in liquid (resin based) raw material which hardens with time. </p>

You can also bring the model and a big box into slic3r, align and orient them (enclose the model in the box), and do a subtract modifier, leaving a hollow where the two intersected. You probably want to do this twice, for a top mould and a botom mould. I've done this, but I don't see any instructions online for it. :(
EDIT: Unfortunately, this would be very tedious. It's much easier to use meshmixer or another publicly available program to subtract one stl from another.
In Slic3r, using another stl as a modifier has no effect unless you are also printing that second stl (normally from another head). So you would have to manually remove all the gcode for the second head. Sorry for the bad advice.