S-Boxes are the key components of many cryptographic primitives and designing them to improve resilience to attacks such as linear or differential cryptanalysis is well understood. In this paper, we investigate techniques that can be used to reverse-engineer S-box design and illustrate those by studying the S-Box F of the Skipjack block cipher whose design process so far remained secret. We first show that the linear properties of F are far from random and propose a design criteria, along with an algorithm which generates S-Boxes very similar to that of Skipjack. Then we consider more general S-box decomposition problems and propose new methods for decomposing S-Boxes built from arithmetic operations or as a Feistel Network of up to 5 rounds. Finally, we develop an S-box generating algorithm which can fix a large number of DDT entries to the values chosen by the designer. We demonstrate this algorithm by embedding images into the visual representation of S-box’s DDT.