Major biological processes rely on the spatial organization of cells in complex, highly orchestrated three-dimensional (3D) tissues. Until the recent decade, most of information on spatial neural representation primarily came from microscopic imaging of "2D" (5-50 mu m) tissue using traditional immunohistochemical techniques. However, serially sectioned and imaged tissue sections for tissue visualization can lead to unique non-linear deformations, which dramatically hinders scientists' insight into the structural organization of intact organs. An emerging technique known as CLARITY renders large-scale biological tissues transparent for 3D phenotype mapping and thereby, greatly facilitates structure-function relationships analyses. Since then, numerous modifications and improvements have been reported to push the boundaries of knowledge on tissue clearing techniques in research on assembled biological systems. This review aims to outline our current knowledge on next-generation protocols of fast free-of-acrylamide clearing tissue (FACT) and passive CLARITY (PACT). The most important question is what method we should select for tissue clearing, FACT or PACT. This review also highlights how FACT differs from PACT on spanning multiple dimensions of the workflow. We systematically compared a number of factors including hydrogel formation, clearing solution, and clearing temperatures between free-acrylamide and acrylamide-based passive sodium dodecyl sulfate (SDS) tissue clearing and discussed negative effects of polyacrylamide on clearing, staining, and imaging in detail. Such information may help to gain a perspective for interrogating neural circuits spatial interactions between molecules and cells and provide guidance for developing novel tissue clearing strategies to probe deeply into intact organ.