Multispectral images contain more spectral information of the scene objects compared to color images. The captured information of the scene reflectance is affected by several capture conditions, of which the scene illuminant is dominant. In this work, we implemented an imaging pipeline for a spectral filter array camera, where the focus is the estimation of the scene reflectances when the scene illuminant is unknown. We simulate three scenarios for reflectance estimation from multispectral images, and we evaluate the estimation accuracy on real captured data. We evaluate two camera model-based reflectance estimation methods that use a Wiener filter, and two other linear regression models for reflectance estimation that do not require an image formation model of the camera. Regarding the model-based approaches, we propose to use an estimate for the illuminant's spectral power distribution. The results show that our proposed approach stabilizes and marginally improves the estimation accuracy over the method that estimates the illuminant in the sensor space only. The results also provide a comparison of reflectance estimation using common approaches that are suited for different realistic scenarios.