One embodiment of the present invention provides a system for profiling a virtual machine on an embedded device. During operation, the system receives an operation-request at a system-level profiler from a virtual machine on an embedded device. The system then records the operation-request in a system-level log. Next, the system sends the operation-request to a native layer on the embedded device. Then, the system receives an operation-response associated with the operation-request from the native layer. The system then records the operation-response in the system-level log. Next, the system sends the operation-response to the virtual machine, thereby facilitating logging of interactions between the virtual machine and the native layer. Note that logging interactions between the virtual machine and the native layer facilitates emulation of the platform independent virtual machine on a second device. Furthermore, note that logging interactions between the virtual machine and the native layer can facilitate emulation of the platform independent virtual machine executing a specific application on a second device.