Methods and reagents for processing samples for fluorescence analysis. Processing methods include treating samples containing riboflavin to reduce riboflavin-dependent autofluorescence by adding riboflavin binding protein to the sample, irradiating the sample, or a combination thereof. Processing methods also include clarifying samples by coagulating, precipitating, and/or otherwise removing proteins and other components that interfere with fluorescence analysis without removing the analyte. Fluorescence analysis methods include fluorescence polarization analysis (FPA) and others. Reagents suitable for performing the disclosed methods are provided.