<p>I just received my E3D v6 hotend and I am installing it on the open source design of a Prusa i3. How do I clean my hotend after each print and after using different filaments?</p>

Usually there is no need to clean the hotend, as filament sticks well to itself rather than to the inside of the hotend. If there are remains - the simplest way to clean it up is to extrude 5-10 cm of new filament, which will gather all remainings clean the hotend.
The above concerns changing filament in the same group of plastic. So if you print PLA you can switch colors/manufacturers and so on without issues. The same goes for ABS.
There is also usually no problem when switching from PLA to ABS.
The worst scenario is to switch from ABS to PLA. This is because the extruding temperature of these two materials is different. Unfortunately ABS can have such a high melting temperature that the PLA will burn. So having a dirty hotend with ABS remainings, there is no way to extrude PLA to clean the hotend because the PLA temperature will not result in melting ABS. It can eventually lead to total plug of HE.
So what can you do when you are in such a situation (ABS -> PLA)?
You can clean the hotend first with ABS. Extrude some, wait until it is cold, ease the springs and pull or tear out the filament from the hotend.
If you are stuck you can use special drills to clean the nozzle.
But to totally omit the issue you can have two hotends :) One for ABS and one for PLA ;) But I think you can manage cleaning if you apply what I've written above.