Since the development of IT technology and electronic commerce, intangible good transactions have played a significant role in international trade. This, in turn, ms led to an increase in intellectual property protection issues. One of the key issues affecting international trade is computer software protection Generally, software is protected by copyright and patent law, i.e. the protection of computer programs is covered by copyright law. There is, however, controversy as to the patentability of software itself and the scope of software protection under existing patent law because of the specific characters of software as subject matter of patents and the negative effects of software patents. This paper examines recent legal situations involving software patents in the United States and the European Union It focuses on these two regions because the U.S. has the most liberal system of software patentability in the world, whereas, the E. U. has the most conservative. In addition, this paper analyzes the positive and negative arguments regarding software patents. This paper proposes changes to the software patent system to reduce the negative effects of software patents and create harmonization in international intellectual property regimes. The proposed methods include the certainty of TRIPs` software patentability connecting with the WIPO patents treaty, the systems for SEMs` protection such as providing insurance or reducing patent costs, and the use of Standard-Setting Organization to maintain open source movement.