I found this technique suggestion in Prusa print community group, so just putting the instructions together for the other users based on what I have learnt there. This technique allows you to use single extruder printers to print multicolor using Prusa Slic3r.
EDIT: It was brought to my attention, there is also a nice tutorial on Thingiverse by user Garfield1970 which I was unaware of at the time writting down this tutorial. He also has some nice sample smiley model there :)
Inkscape - bitmap tracing
Fusion - 360 3D model/stl export
Prusa Slic3r and a 3D printer :)
Step 1: Model Preparation
To prepare the model from scratch or including your own graphics I recommend to watch THIS video tutorial from Make Anything YT channel - basic to slightly advanced knowledge in F360 required. To trace bitmap to vectors to be later used in F360 as .dxf I suggest Inkscape as its a free alternative, but any SW that can export vectors would do. In F360 I highly recommend "Check sketch" plugin which helps to close faces for extrusion.
Step 2: Slic3r Preparation (Printer Settings)
Open your Prusa Slic3r and go to Printer settings to add additional extruder/s. Another thing to do under Printer tab is setting M600 in Custom G-code tab -> Tool change G-code. Set also different colors for each extruder under this tab, to make the color assignment later easier.
Step 3: Slic3r Preparation (Color Assignment)
When you move to your plater tab, you should be able to see 2 materials now, each for one of the extruders and their color alignement as set in previous step.
If you have separate models prepared, adding them both on platter now will generate a multipart pop up which you can accept and the colors are assigned automatically.
If you did the changes to printer settings after the model was imported, you can assign extruder via the object settings. Set the desired extruder for all perimeters and infills for the given object.
Slice, export g-code, print and enjoy the results :)