Before we jump right in we best think of a mod! If you've already thought of one, please skip this section.

Lets take for example.. a mechanic from the game BaroTrauma!

He'll fit the proportions pretty well and can be customised easily.

Right click Hidden Deep, Click Properties, Click "Local files", Click Browse Local Files.
Alternatively you can go through windows explorer like a madman and find it there.
You should now be in the folder "Hidden Deep Playtest", Make your way from this folder to "\graphics\miner1\b\horiz" for this is the place our graphics for Murphy and his buddies is stored.

Alright, so we can assume you have some sort of editing tool. Paintnet, Photoshop, Gimp or even simple paint can do with enough elbow grease.
Here's my experience from Paintnet, A software that has a handy dandy layer feature!
REMEMBER TO BACKUP YOUR IMAGES
1. Open your image in Paintnet
2. Find the mod image you want (Lets say, a torso)
3. Paste your mod image in as a new layer.
4. Fit the mod image onto the base image (Remember to make the torso not too fat!)
5. Delete bottom layer.
6. Save into the Horiz folder
Repeat steps with all items (Yes, including gore items, you can just use the non-gore one if you dont have one with gore) until character is fully modelled.

Launch Hidden Deep (Of-Course) and get into a campaign, you should see Murphy is someone.. different, he could be some mechanic, Spiderman wearing jordans, Barney from HL1 or even just a blob of flesh.
If something you find is wrong (IE. Murphy's torso is 50 times the size of texas) you can always edit it in paintnet!

Have fun!

Weapons are stored in \graphics\weapons
Sound files are stored in \sounds
Pistol and SMG use same firing noise!
Murphy's sounds are stored in \sounds\miner
Murphy and Hannigan (Other dude) share the same faces and hands.
Murphy (Main character) is the one in the BROWNISH suit, Hannigan is in the ORANGE suit!