Chris builds and paints Warhammer 40k models and regularly produces blog posts showing how he's produced his latest masterpiece. He often replaces parts with clear resin casts he makes to allow for LED lighting to shine through and modifies the bases so they can accommodate the battery holder, switch etc without needing to be any deeper.
This model used a resin case for the data pad on the arm but the eye was just drilled out. Chris used one of our Warhammer 32/40mm base lighting kits for this model. He drilled out the middle of a 32mm base leaving only the edge so the PCB could fit in inside and used modelling putty to hold it in place and form a rocky area for the model to stand on.
Holes are then drilled through the model to route the wiring for the LED lighting kit.
Other techniques include using Green Stuff Splash Gel, which looks a bit like a thick acrylic medium, which can be built up in layers to form flares from guns etc and looks very effective when painted.
A nano or 0805 chip LED is threaded through the gun so that when lit it looks like the gun is firing. The eyes are lit with a Nano chip LED threaded through into the head. The eyes are drilled out.
If you would like a shorter nano or 0805 LED for this purpose just ask.