Microscopy is widely used for brain research because of its high resolution and ability to stain for many different biomarkers. Since whole brains are usually sectioned for tissue staining and imaging, reconstruction of 3D brain volumes from these sections is important for visualization and analysis. Recently developed tissue clearing techniques and advanced confocal microscopy enable multilayer sections to be imaged without compromising the resolution. However, noticeable structure inconsistence occurs if surface layers are used to align these sections. In this paper, a structure-based intensity propagation method is designed for the robust representation of multilayer sections. The 3D structures in reconstructed brains are more consistent using the proposed methods. Experiments are conducted on 367 multilayer sections from 20 mouse brains. The average reconstruction quality measured by the structure consistence index increases by 45% with the tissue flattening method and 29% further with the structure-based intensity propagation.