First of all: there is no reason why SERS wouldn't work in a confocal setup and your excitation wavelengths are also standard appropriate quantities.

Regarding a fluorescence: if you have fluorescences from your material that affect the spectral range with both of your excitation wavelengths, that's bad luck and you won't get rid of it. You can play a little with the excitation power and see if your desired peaks get better, but that's about it. Be aware that SERS often has a strong signal of its own, so depending on your substrates that might be normal.

If you have luminescence due to degradation of the optical fibre (that may happen), tilt the sample a little so you have less Rayleigh line heading for the notch filter. But if your fibre degrades, it should be changed anyway (don't do that alone if you're new).

You want to use a confocal optical microscope scheme from samples labeled with fluorescent tags. Then the device can be called a fluorescence confocal microscope. SERS is Raman spectroscopy of molecules adsorbed on the surface of silver or gold nanoparticles. In contrast to conventional Raman spectroscopy, SERS gives spectra with scattering intensities thousands of times larger than those obtained with conventional Raman spectra. Fluorescence reduces the intensity of SERS and they seek to get rid of it. Therefore, it is not clear what you want to have.

My samles (Proteins, Polyphenols) have a strong autofluorescence.

I‘ve read that SERS is able to reduce fluorescence and enhance the raman scattering. Thats what I want. At the moment I only get fluorescence noise without (or a few very small) peaks. I already tried to synthesise AuNp‘s and fix them on a ITO glass slide. Then I put my sample on the AuNp slide and focus the sample particle with the microscope.

Use the 785 nm excitation with gold NPs to minimize fluorescence.

Dear, Joseph Heintges,

Yes, You can do with Confocal.

Selection of wavelength important Your laser Wavelength that match with your Nanoparticles absorption range 785 with Gold may reduce the fluorescence of your molecule. You have to tune your laser power and distance b/w your SERS substrate and laser. Then fix it for further analysis. More particularly you have to take your analyte concentration form low concentration to high concentration.

Confocal lasers work best for a flat homogeneous SERS substrate so that you do not have to realign the laser confocal plane everytime. SERS substrates can function well under multiple laser wavelengths if their building block nanoparticles can adapt to the wavelengths.

---------------------------------

High quality Silver (Ag) nanocubes and Surface-enhanced Raman Scattering (SERS) substrates available at:

https://silverfactorytechnology.com/