This paper investigates the design of a potential Software Defined Radio (SDR) based prototype for Filter Bank based Multi-Carrier Transmission. It allows for implementing and testing transmitter and receiver in real-time on Universal Software Radio Peripheral (USRP) by using two USRP boards. Additionally, an implementation of some classic channel models in a separate USRP board has been used for emulating a propagation channel. The presented prototyping system supports FBMC waveform but also Orthogonal Frequency Division Multi-carriers(OFDM) one using MATLAB routines. With this motivation, we propose a study on real-time decoding of Offset Quadrature Amplitude Modulation FBMC (OQAM-FBMC) radio frames. In this system, data recovery at the receiver is very sensitive to time and frequency synchronization of the frames. This problem was addressed in many theoretical research works. However, considering its practical aspects in the context of a realtime radio transmission, a signal processing block is required to satisfy a trade-off between the accuracy and the latency. We especially recognize different limits, imposed by both hardware and software entities, to the real-time system.