Self Organizing Map (SOM) is a neural network that is effective in classifying patterns that form the feature map by extracting characteristics of the input data. In this study, we propose an algorithm to determine the cell formation and the machine layout within the cell for the cell formation problem with operation sequence using the SOM. In the proposed algorithm, the output layer of the SOM is a one-dimensional structure, and the SOM is applied to the parts and the machine in two steps. The initial cell is formed when the formed clusters is grouped largely by the utilization of the machine within the cell. At this stage, machine cell are formed. The next step is to create a flow matrix of the all machine that calculates the frequency of consecutive forward movement for the machine. The machine layout order in each machine cell is determined based on this flow matrix so that the machine operation sequence is most reflected. The final step is to optimize the overall machine and parts to increase machine layout efficiency. As a result, the final cell is formed and the machine layout within the cell is determined. The proposed algorithm was tested on well-known cell formation problems with operation sequence shown in previous papers. The proposed algorithm has better performance than the other algorithms.