The availability of Infrastructure-as-a-Service (IaaS) computing clouds gives researchers access to a large set of new resources for running complex scientific applications. However, exploiting cloud resources for large numbers of jobs requires significant effort and expertise. In order to make it simple and transparent for researchers to deploy their applications, we have developed a virtual machine resource manager (Cloud Scheduler) for distributed compute clouds. Cloud Scheduler boots and manages the user-customized virtual machines in response to a users job submission. We describe the motivation and design of the Cloud Scheduler and present results on its use on both science and commercial clouds.