  Molecular clouds are a fundamental ingredient of galaxies: they are the
channels that transform the diffuse gas into stars. The detailed process of how
they do it is not completely understood. We review the current knowledge of
molecular clouds and their substructure from scales $\sim~$1~kpc down to the
filament and core scale. We first review the mechanisms of cloud formation from
the warm diffuse interstellar medium down to the cold and dense molecular
clouds, the process of molecule formation and the role of the thermal and
gravitational instabilities. We also discuss the main physical mechanisms
through which clouds gather their mass, and note that all of them may have a
role at various stages of the process. In order to understand the dynamics of
clouds we then give a critical review of the widely used virial theorem, and
its relation to the measurable properties of molecular clouds. Since these
properties are the tools we have for understanding the dynamical state of
clouds, we critically analyse them. We finally discuss the ubiquitous
filamentary structure of molecular clouds and its connection to prestellar
cores and star formation.
