In the field of tissue engineering, design and fabrication of precisely and spatially patterned, highly porous scaffolds/matrixes are required to guide overall shape of tissue growth and replacement. Although rapid prototyping fabrication techniques have been used to fabricate the scaffolds with desired design characteristics, controlling the interior architecture of the scaffolds has been a challenge due to Computer-aided Design (CAD) constrains. Moreover, thick engineered tissue scaffolds show inadequate success due to the limited diffusion of oxygen and nutrients to the interior part of the scaffolds. These limitations lead to improper tissue regeneration. In this work, in order to overcome these design and fabrication limitations, research has been expanded to generation of scaffolds which have inbuilt micro and nanoscale fluidic channels. Branching channels serve as material delivery paths to provide oxygen and nutrients for the cells. These channels are designed and controlled with Lindenmayer Systems (L-Systems) which is an influential way to create the complex branching networks by rewriting process. In this research, through the computational modeling process, to control the thickness, length, number and the position of the channels/branches, main attributes of L-Systems algorithms are characterized and effects of algorithm parameters are investigated. After the L-System based branching design is completed, 3D tissue scaffolds were fabricated by “UV-Maskless Photolithography”. In this fabrication technique, Polyethylene (glycol) Diacrylate (PEGDA), which is biodegradable and biocompatible polymer, was used as a fabrication material. Our results show that L-System parameters can be successfully controlled to design of 3D tissue engineered scaffolds. Our fabrication results also show that L-System based designed scaffolds with internal branch structures can be fabricated layer-by-layer fashion by Maskless Photolithography. This technology can be easily applied to engineering living systems.