A design file can get larger in size as the complexity of the target object increases. A large design file may reside in a large parallel computing system, such as cloud computing systems, and many designers may work concurrently on the same design file. In such a case, it is obvious that we need some kind of protection mechanism so that each user can access only the area of the file he or she is entitled to. Two approaches can be taken for this problem: one is the traditional access control mechanisms and the other encryption techniques. We take the latter approach to ensure the safety of the file even in public domain such as clouding systems, and in this paper, we suggest an encryption scheme for a file where the file is encrypted in multi-layer so that each user is allowed to access the file only at the layer for which the user has the proper access right. Each layer of the file is encrypted with different keys and these keys are exposed only to those who have the right access permit. The paper explains the necessary file format to achieve this goal and discusses the file manipulation functions to handle this new file format.