question about software patents

There isn't really a separate "software patent". In the US, where I am guessing you would file, a software patent is just the same utility patent that is used for any other invention. However, having said that, there is an art to writing a patent that will adequately protect a software invention and will be granted by the patent office. This is especially true because the Supreme Court has had several recent rulings that make it even trickier to get patents for software. If you decide to file a patent, I would highly recommend finding an attorney who has experience in preparing and litigating software patents, and if possible, one with experience in your field (3D CAD and databases).

About your second question, patents don't really provide any "protection" against copying. A granted patent gives you the right to sue for infringement. Patent lawsuits that go to trial end up costing $1 million to $2 million, so as a startup, your motivations in getting a patent are usually:
1. giving you ammunition for a counter-suit if you are sued for infringement by a competitor
2. adding value to your company in an acqusition or financing
3. putting competitors on notice that they are taking a chance if they copy your technology and it is successful
4. giving you the option of licensing your technology as a potential additional revenue stream
5. showing the outside world that you are serious about the value of your technology
These are all very valid reasons, and I always advise startups to have at least one patent. However, the patent should always be part of an overall strategy for intellectual property, which should include having trade secrets and continuing development to stay ahead of the competition.

On your third question, the cheapest way to protect intellectual property is usually through trade secrets. However, this is often not the most effective strategy in software because of the relative ease of reverse engineering the product. One option to hold down costs for a startup is to file a provisional patent application. The patent office does not examine a provisional application, but it secures a priority date for the disclosure that is described, and the patent office fees are only a few hundred dollars. I would warn you not to fall into the trap of filing an inadequately prepared provisional application, however, because a later patent application can only use material described in the provisional application. If there is ever any litigation, one point of attack is discrepancies between the provisional application and the full application. Most attorneys will give you a quote on preparing and filing a provisional application; the fees vary but it is usually around a few thousand dollars.

Just one additional note to what Alan has stated in order to make things a bit clearer - a patent does not give you, as the patent holder/owner, the right to make, use, or sell your own invention - patent gives you, as the patent holder/owner, the right to exclude others from making, using, or selling the patented invention. So if you have a patent on particular software, and someone is "copying" it, as Alan noted, you have to sue them for patent infringement. This is a common misconception about patents - people, in general, believe that once they have a patent on something, they themselves can automatically make, use, and sell the patented device, system, method, whatever, but that is not true - you prevent others from doing so.