Polyetheretherketone is a promising material for implants due to its good mechanical properties and excellent biocompatibility. Its accessibility to a wide range of applications is facilitated by the ability to process it with an easy-to-use manufacturing process such as fused filament fabrication. The elimination of disadvantages associated with the manufacturing process, such as a poor surface quality, is a main challenge to deal with. As part of the mass finishing process, centrifugal disc finishing has demonstrated good results in surface optimization, making it a promising candidate for the post-processing of additively manufactured parts. The objective of this study is to identify the key parameters of the centrifugal disc finishing process on the waviness of additively manufactured PEEK specimens, which has not been investigated previously. The waviness of the specimen was investigated by means of confocal laser scanning microscopy (CLSM), while weight loss was additionally tracked. Six parameters were investigated: type, amount and speed of media, use of compound, amount of water and time. Type of media, time and speed were found to significantly influence waviness reduction and weight loss. Surface electron microscopy images demonstrated the additional effects of deburring and corner rounding. Results on previous studies with specimens made of metal showed similar results. Further investigation is required to optimize waviness reduction and polish parts in a second post-processing step.