The electrochemical properties of micro and nano-electrodes are widely investigated due to their low faradaic and capacitive currents, leading to a new generation of smart and implantable devices. However, the current signals obtained in low-dimensional devices are strongly influenced by noise sources. In this paper, we show the evaluation of filters based on Fast Fourier Transform (FFT) and their implementation in a graphical user interface (GUI) in MATLAB®. As a case study, we evaluated an electrochemical reaction process of charge transfer via outer-sphere. Results showed successful removal of most of the noise in signals, thus proving a promising tool for low-scale measurement.