In an apparatus and method for protecting resources of a computing system from a malicious code by selective virtualization, at least a part of the resources is classified as compulsory resources for executing a program on the computing system. When a vulnerable program executed in a separate space attempts to access one of the compulsory resources, an operating system level virtualization is performed. Further, when the vulnerable program attempts to access one of the resources of the computing system which is other than the compulsory resources, the vulnerable program is permitted to access a modified resource which is generated by modifying content of the resource.