Monitoring the functional behavior of an application is an important capability that assists in exploring the performance of a target application against different SW/HW implementations. Recently, there have been efforts to exploit the ability to trace the internal signals of the soft-core processors for developing FPGA-based profiling tools to monitor programs running on these processors. However, these previously developed techniques are application-dependent, i.e., they require the designer either to edit the HDL code or the application code to obtain the desired trace information when targeting new applications. In this research, we propose an application-independent profiling technique using the MicroBlaze/FPGA platform where profiling library or user-defined functions can be achieved by tracing the unique instruction flow that distinguishes functions from each other rather than monitoring the program counter value (the addresses of the functions). Hence, modifying the application code or targeting new application does not require reconfiguring the FPGA or modifying the application code for targeting the same functions. This technique can be used to analyze the target application at the source code level, observing the dominant operations and demanded resources that characterize the system behavior. In addition, this technique can assist in selecting the appropriate processor architecture for a given application by considering MicroBlaze as a reference architecture from which the functional behavior of the target application can be mapped to the performance of other architectures.