High bit rate transmission over polymer optical fiber (POF) attracts great interests recently. This paper investigates the discrete multi-tone (DMT) transmission over 50-meter stepindex POF (SI-POF) based on an experimental system. The system adopts a digital storage oscilloscope (DSO) and processes the data off-line, which is the most common solution in the POF researches. We first study the problem of effective number of bits (ENOB) in the DSO's analog-to-digital converter (ADC). Then we investigate the optimum configuration of the DMT transmission in terms of subcarrier number selection, clipping and ADC quantization effect mitigation. The proposed method of selecting optimum configuration can be easily applied to any other DMT over POF systems.