I have noticed that on some boxcars there is damage to the roof from a forklift; looking like the roof was bubbled. Does anyone have a good method to model this?
You would need to gently soften/melt the plastic and push up to make the bubble. You could use one of those butane lighters with the long tube the dollar stores sell. I think they sell them to light grills. Turn the flame down real low if you do this and maybe practice on and old junk car.
Jim
Practicing on the junker car is good advice – this “melt the plastic and deform it with a blunt stick” technique has a high failure rate as I can testify 
The smell is not so pleasant either by the way. Work in a ventilated area.
Many years ago a guy showed me an HO hopper car with the most realistic bulges I had ever seen. He was embarassed to tell me how he did it – he intended to secure a load of plastic “coal” and used the wrong kind of cement – it attacked and deformed the plastic but it created very realistic bulges and dents. Of course it is almost impossible to control such a technique so if it works it is probably pure luck …
I have NOT tried another technique (so probably I should say nothing about it, but what the heck, right?) but I wonder if thin metallic foil could be pressed and burnished on selected roof sections with something small underneath – say, thin pieces of styrene glued to the roof – to give it the required “bump” up. There is a metallic burnishing foil that I have seen in the MicroMark catalog that could be the right stuff. If it worked this would really give good control over the results, although again you might want to practice on a junker since it still involves doing something to the car itself. This idea is not entirely original with me, by the way. Some guys have used an idea like this to model and simulate wreck damage (replace a plastic end or roof or side panel of a box car with a foil version that can be bent and dented in a prototypical manner). Somehow the slightly melted plastic technique never quite looks as much like bent and bulged metal as does bent and bulged metal, I guess.
Now yet another technique, assuming we are talking about a standard transition era 40 or 50 foot boxcar here, is to find an old Athearn metal kit, later reissued by Menzies in the 1980s, or a similar metal kit from Varney, and carefully replace t