Femtosecond (fs)-laser processing of CdSxSe1-x-doped borosilicate glasses was investigated to create hybrid multiscale structures consisting of semiconductor nanocrystals embedded in microscopic domains defined by the laser irradiation. Laser processing was carried out with both low (1 KHz) and high (1 MHz) repetition rate fs-lasers using pulse fluences between 2 and 2000 J/cm2 and sample scan speeds ranging from 0.05 to 4 mm/s. The samples were subsequently heat-treated at temperatures between 500 and 600°C and characterized using optical microscopy, electron microscopy, wave dispersive x-ray spectroscopy (WDS), and confocal fluorescence microscopy. For 1-KHz laser processing conditions, nanocrystal precipitation showed no significant distinction between the modified and unmodified regions in the sample. Using a 1-MHz pulse repetition rate laser, however, we introduced chemical inhomogeneity across microscopic modifications, forming three chemically distinct regions: sodium and potassium-rich, zinc rich, and silicon rich. These regions exhibited different semiconductor precipitation dynamics, with the sodium and potassium-rich region showing strong preferential precipitation of cadmium sulfo-selenide nanoparticles, thereby localizing quantum dot precipitation to these chemically defined microcrucibles in the glass.