Any text editor will do
Changing Mat files
STEP 1:
Just open the desired .3do file in a text editor like
Notepad, Wordpad or Write.
(I usually use the "ky.3do" as a template).

STEP 2:
Notice that for each "parts" like arms, neck, torso, etc
there is a name for a .mat file.
STEP 3:
All you need to do is change the name of that Mat to another.
If you can't guess which particular texture the name refers to
just use an extractor like "ConMan" or GobExplorer" to extract
that particular Mat file or look in the Mats section
STEP 4:
You don't have to stick to standards. Be creative!
Adding new Mat files
Easy as clubbing an Ewok!
STEP 1:
Simply create a new directory called "mat"
inside the "ressource" directory in JK or MotS.
STEP 2:
Then put the desired .mat file in it
STEP 3:
Don't forget to add them in a .3do file if you
wish to use those new textures in the game.
Using the new 3do file in Multiplay
Everyone must have a copy of your new .3do file
if they are to see your character.
Adding the new .3do file to the Models.dat file
Here's what you have to do on order to use your new 3DO file.
STEP 1:
Simply create a new directory called "misc"
inside the "ressource" directory in JK or MotS.
STEP 2:
Then put your "Models.dat" file in it. This is the file that indicates
to the game engine which 3do (your skins) file goes where.
STEP 3:
Open the "Models.dat" file in a text editor.
Simply add another line at the end or change one of the existing line.
If you just want to change a 3do file, all you need to do is substitute the
name for the particular .3do file you want to change to.
Important: Do not forget to add a number to the "numModels"
at the top of the Models.dat file evertime you add a new 3do.

STEP 4:
Then create another directory called "3do"
inside the "ressource" directory in JK or MotS
and just put your custom .3do file in it.
That' all!
Modifying the actual sections of a 3do files
This is for those who want to create a new model,
like I did with the Twi'Leks or the Ithorian Renegade
STEP 1:
Scroll down to the desired section. In this case the HEAD section
You have to copy a section starting from the top:

STEP 2:
Scroll down to the end of that section until you
reach the next MESH section
Cut and paste that section to the 3do
you want to modify

STEP 3:
In the material section, you have to change
the numbers in row 2. This will tell the game
which Mat to put where. They correspond to the
numbers in the "Material List"at the start of
your 3do file.

STEP 4:
For all multiplayer models, you have to repeat
the procedure three more times for each sections
of the same MESH.
You can repeat the same section four times
if you wish. The file is bigger, but I've
never encountered problems with that.