In Fourier domain optical coherence tomography (FDOCT) coherence noise is caused by interference of light waves back-reflected or scattered from different spots within a measuring depth or from optical components within the OCT system such as a bended optical fibre. This coherence noise appears as periodic stripe patterns along the axial direction in resulting images. Background subtraction and physical segmentation are used to degrade the periodic coherence noise in previous studies. Here we utilise a post-processing method by applying a frequency domain filter to reduce the periodic coherence noise. Even though the approach taken is a very simple one, it visibly removes the periodic coherence noise from FDOCT images without influencing the original measured objects. The edges and textures of the objects in the processed image are identical as in the original image. The signal to noise ratio is also enhanced by using frequency domain filtering. Applying frequency domain filtering to FDOCT image can reduce the periodic noise significantly. This method is an easy, efficient way to improve the image quality without calibrating the system or measuring the background noise each time before a measurement.