I've a 180 gallon that I acquired earlier this year, it was a reef tank in a previous life and I had no qualms using it for freshwater.
If your worried about it, give it a though cleaning, since it's only 40 gallons, plus some if your using a sump, you can easily fill it up with hotter warm water, not hot but not quite warm in between those, and treat with a variety of things, bleach, H2o2, or vinegar. When I set up my converted tank I put two gallons of vinegar in it and let that cycle through for a week, since my setup is almost 220 gallons I couldn't use hotish water had to use cold, but I put a bunch of heaters in there and cranked it up to almost 90 degrees for that week. Bleach would probably be your best bet, it pretty much kills everything and thoroughly disinfects the aquarium, if you do use bleach just make sure you drain all the bleachy water out, replace with clean water, and treat with Prime or a similar chemical. I usually double dose my Prime when I clean stuff with bleach just to be on the safe side.
If you are worried about it, replace the substrate. If your tight on cash you can probably sell the skimmer it came with fairly quickly, around me those things go fast on the saltwater forums.