i get the electrons to a higher level state, then i want to measure the emission/fluorescence.
how can i separate between the signals if they are both happening?
How do you separate what signals? If you mean fluorescence from the incident radiation, you either take advantage of a combination of geometry, filters, or the Stokes shift (wavelength difference). If you mean emission from fluorescence, you don't - in most contexts they mean the same thing. Technically, emission can include some things that aren't fluorescence. E.g., a molecule can fluoresce and phosphoresce at the same time, and we'd refer to both of these as "light emission". You can distinguish these in a few easy ways, often just by inspection - what wavelength the signatures show up at. Phosphorescence is also often better observed at low temperature. The true way is to do time-resolved experiments, because the process rates are different.
If none of this is what you want to know, then you'll have to be more specific with the wording of your question.