Heterogeneous platforms with FPGAs have started to be employed in the High-Performance Computing (HPC) field to improve performance and overall efficiency. These platforms allow the use of specialized hardware to accelerate software applications, but require the software to be adapted in what can be a prolonged and complex process. The main goal of this work is to describe and evaluate mechanisms that can transparently transfer the control flow between CPU and FPGA within the scope of HPC. Combining such a mechanism with transparent software profiling and accelerator configuration could lead to an automatic way of accelerating regular applications. In this work, a mechanism based on the ptrace system call is proposed, and its performance on the Intel Xeon+FPGA platform is evaluated. The feasibility of the proposed approach is demonstrated by a working prototype that performs the transparent control flow transfer of any function call to a matching hardware accelerator. This approach is more general than shared library interposition at the cost of a small time overhead in each accelerator use (about 1.3ms in the prototype implementation).