My way of doing it is a bit long but, I usually open SimPE and then on the Tools Menu, under Neighborhood click Neighborhood Browser and find the Hood you want and open it, wait for it to load and then again on the Tools Menu under Neighborhood click Sim Surgery. Find the Sim you want to change from in the left pane and click on it, then in the right pane under Patient Sim, click use. Now click Export and then Save. Close SimPE.
Why I clone the original Sim is so I get the same colour hair, eyes and similar skintone, rather than go off memory.
I also use Repacement Faceplates rather than Maxis.
Now I open Bodyshop, find the Sim I want to do a make over to and Clone it. After you have finished cloning go back and delete the original Sim. Close Bodyshop.
Now start your game and go to CAS in the Hood the new Sim is in and create your Sim, I usually pick the same first name and change the last letter of the Surname, as it doesn't matter as this Sim will end up deleted anyway. Do any tweaking now and finish off with Save. You can close your game now.
Open SimPE and then on the Tools Menu, under Neighborhood click Neighborhood Browser and find the Hood you want and open it, wait for it to load and then again the Tools Menu under Neighborhood click Sim Surgery. Find the Sim you want to change from in the left pane and click on it, then in the right pane under Patient Sim, click use. Now find the Sim you are going to change to and click on it, then in the right pane under Archtype Sim, click use. Now click Sim Surgery at the bottom. Now click Save package on the top Menu Bar. Close SimPE.
Now go back in game, check your Sim has been changed and then delete the Sim in the Sim Bin.
If your game takes a while to load plan how to do the above by doing multiples.
With 7Gb of CC mine takes about 4 minutes to load, good luck.
EDIT:
I found a version of this with pictures by wirelessguy over at Insim, but you might have to register if not a member.
http://www.insimenator.org/index.php/topic,18184.0.html