Scott Cawthon primarily used Clickteam Fusion (formerly known as Multimedia Fusion) for developing his early games and the original "Five Nights at Freddy's" titles. Clickteam Fusion is a 2D game engine known for its ease of use and rapid prototyping capabilities.

Scott Cawthon used various 3D modeling and animation software to create the characters and environments in his games. While the specific software he used is not always explicitly stated, it is evident that he had proficiency in 3D modeling, texturing, and animation techniques.

In addition to Clickteam Fusion and 3D software, Scott Cawthon likely used other game development tools for tasks such as sound design, level editing, and scripting. The specific tools may have varied depending on the project.