We present our recent multi-molecule ALMA observations of giant molecular clouds (GMCs) in local galaxies, e.g., NGC 1068, M33, and other galaxies. GMCs are essential structures as the site of massive star formation. Classically, GMCs have been identified as topologically-closed "islands" in a 3-dimensional cube of a bright emission line such as 12CO(2-1) and 13CO(1-0). All subsequent analysis and characterizations of GMCs are based on such cataloged clouds identified by single-line observations. However, such an emission line is observed as the results of a complex combination of physical and chemical parameters such as density, temperature, pressure, ionization degree and molecular abundance of the molecular cloud. In other words, it merely represents a limited aspect of the complex physical and chemical structures of the true molecular clouds. Using the recent multi-molecule (e.g., 13CO, C18O, HCN, HCO+, HC3N) data sets of a few local galaxies with the spatial resolution of < 100 pc and a hierarchical Bayesian analysis, we derived 3D cubes of physical quantities, i.e., kinetic temperature and gas densities, and chemical compositions. Then, we identify the 3D structures based on the derived physical quantities such as the gas density ("physically-identified cloud structures" hereafter). In this presentation, we will present a detailed comparison of the properties of physically-identified cloud structures and line-intensity-selected (i.e., 12CO and/or 13CO-based) clouds. We will also report the relationship between the properties of physically-identified cloud structures and global structures of galaxies, such as the bar, spiral arm, and so on.