—In this paper we propose a virtualization layer to handle the program execution on reconfigurable computers in order to address one of their biggest problems which is the management of the reconfigurable hardware in a multitasking environment. The virtualization layer is responsible for allocating the hardware at run-time based on the status of the system. Furthermore, it provides a consistent and low overhead interface to decouple the process of software development from hardware design which will result in the software to be independent of the underlying reconfigurable hardware. This paper discusses the virtual layer’s specification and components. Our preliminary results for a prototype simulated on Molen hardware organization show a competitive performance comparing with an optimal hardware allocation. Keywords-component; run-time support, reconfigurable computers, virtualization