We demonstrate a normalization method for removing noise introduced into optical in sial measurements by sample rotation wobble;during molecular beam epitaxy. The technique consists of measuring the angle of rotation of the sample through optical triggers attached to the sample manipulator rotation drive, acquiring a normalization curve at the various trigger points, then applying the normalization appropriate to each trigger to subsequent data. This cyclic normalization is demonstrated on normal-incidence optical reflection data and atomic absorption measurements in which the flux-monitor light beam is reflected from the sample to allow determination of layer thickness in addition to atomic flux. Noise reductions by factors of 3 to 30 were observed in both systems, with the larger improvements for samples with larger wobble angles, while preserving the original time resolution of the data. We achieve normalized optical reflectance data with a noise standard deviation of 1% over a period of one to two hours and similar results for atomic absorption data on shorter time scales. The technique is limited by the long-term mechanical stability of the manipulator and collection optics.