A bit of a late reply, but better late than not I guess.
@Habboi: he wants differently skinned Barney's all in the same map. Some skin replacement isn't going to cut it, allas.
@bal: I'm going to explain how to do this with Milkshape 3D. It has a 30 days trial version so you'd better learn fast.
Anyway, you must decompile both the original barney model and the custom one. In Milkshape's Tool menu, go to Half-Life and click Decompile Normal HL MDL File. Open the model and click ok, then click ok on the next dialog that pops up (leave all things ticked). You'll end up with a crapload of .smd files, a few bitmaps and a .qc file. Decompile the other model just as you did with this one, but we only need the reference .smd files and textures from that one, so untick the other two boxes.
Now open the .qc file in a text editor. It's a pretty large file, but we only need a little of info from it. Search for '$bodygroup studio'. It should contain the line 'studio "BARNEY-X_Template_Biped1"' between accolades. Notice the other bodygroup, called gun, which contains 3 lines. That's because Barney can swap it's gun bodygroup: one of the lines has the gun mesh attached to the hand, another one has it placed in the holster and the last one is empty (for when Barney dies). The soldiers and scientists use this system as well: it allows them to use the same body, but different heads and weapons. Essentially it's a modular system.
Well, the idea now is to add some other Barney bodies to it's studio group (because that contains his body). You decompiled the custom Barney and got it's reference .smd's. Find out which one contains the body (you can import them into Milkshape to view them). Give it a different name to avoid name conflicts, and add a line to the .qc file, inside the two accolades, that refers to it's filename.
Now, go to Milkshape's Tools menu, to Half-Life and select Compile QC File. Select the .qc you just modified and hit go. If everything went right, you should now have a new barney model, containing a different body, which you can select with the 'body' key that you manually add to your monster_barney entities.