In order to validate rotordynamical models vibration measurements in noisy environments leading to poor quality are in many cases necessary e.g. on-site measurements. For rotordynamical systems not only unwanted broad banded noise but also distinct frequencies are often present e.g. due to unbalance. The aim of this paper is therefore to suggest a noise reduction method in order to increase the quality of such vibration measurements. Both random noise and distinct frequency noise are applied on a finite element model of the rotor system. First, vibration data is stored when the system is running only with the noise as excitation source. Then a known input (i.e. a shaker) is added and the vibration data is stored again. Finally, the noisy signal is subtracted from the one with known input in the frequency domain. This noise reduction method significantly increased the coherence.