Silicon nanostructures can be prepared by different methods that considerably change their optical properties depending on experimental conditions. They are also very sensitive to molecular environment and external influences that can be used for multiple applications in different areas. Silicon nanostructures prepared by laser ablation show large perspectives for molecular sensing and biomedical applications. In this paper, an overview of optical properties of silicon nanostructures with focus on nanoparticles prepared by ultrafast laser ablation in liquids is provided. It is shown that they reveal wide prospects for applications in nanobiomedicine and their unique characteristics can be significantly enhanced due to laser-induced metal incorporation. Metal inclusions lead to appearance of plasmonic properties in semiconductor nanomaterials that can be applied for molecule detection using surface enhancing of optical response.