Question: If the USPTO grants me a patent on software, will courts use similar standards in upholding my invention as being patentable?

Answer: Yes. Courts have followed the Alice guidelines in finding software inventions patentable. In fact, observers have found that many courts are broader than the USPTO in their approach to patentable subject matter.
Just months after Alice, the Federal Circuit determined an invention directed to an e-commerce system to be patentable. Similarly, the court in Trading Technologies v. CQG applied the Alice standards in finding a method for trading stocks on an electronic exchange to be directed to patent eligible subject matter.
In Trading Technologies, the court focused on the inventive concept of the invention: keeping the prices of stocks static in position, and instead allowing the quantities at each price to change. This inventive concept solved a problem with electronic exchange trading, specifically the risk that a trader would miss an intended price as a result of the stock price changing during the time between which the trader typed the order and the time the order was filled. Notably, this inventive concept “allowed some traders the ability to more efficiently and accurately place trades on electronic trading systems.”
Thus, like the USPTO and the PTAB, courts protect the property rights of software innovators.