First you need to export the model as .md3, there are some export scripts for that somewhere. Then you need to find the model you want to replace in your base/data-1.1.0.pk3 (it's actually just a .zip, tho don't mess with this file). Then you put your model in the same path/subfolder which you create, then zip it up and rename to z-mymod.pk3. For example to replace data-1.1.0.pk3/models/weapons/rifle/rifle.md3 you create your own rifle.md3, then make folders models/weapons/rifle/ and put it in there, then zip it, then rename to z-newrifle.pk3. You will only be able to see your own model on unpure servers and local server ('/devmap atcs' for example).