Hi, Carlos. Nowadays, this is one of the most important goals in 3D printing. Biodegradable tissue engineering scaffolds require new development of polymeric composite materials.
For biodegradable polymers, you want to look into HIPS filaments and PVA (also called PVOH and PVAl) filaments. I assume by scaffolds you mean sacrificial support? PVA would be the perfect choice for you, then, because it is soluble simply in water and is biodegradable. It can have issue with having PLA and other common printing materials stick to it, but it is typically worth it once you sort out your printers setting. Once the print is done you can sink the whole thing into water and the PVA will dissolve away. HIPS is also a solid choice if you have issues with PVA filament; HIPS dissolves in a solution of Limonene (and is also biodegradable). For both filaments, you basically need to have a dual-extruder 3D printer, so that one nozzle prints only support material, and the other prints your "actual" material, such as PLA or ABS or Nylon or what have you.