I'm not exactly sure I understand your question completely, but in the most basic sense: if you have two samples (crystal, glass, etc.) that are made of the same material but have different color, this means that there is some difference in the kind of dopant present in the matrix/lattice/etc. that changes its apparent color. This color change is itself a sign that the absorption/transmission properties of the material are different.
A common example is aluminum oxide: when pure and undoped, the crystal is clear; when doped with elements like chromium ions, titanium ions, and iron ions (and others), the apparent crystal color may become red, pink, yellow, blue, etc. because of the change in the optical properties of the material.
If you have a black-colored glass and a transparent glass, this could mean that there are dopants inside the black-colored glass that are absorbing the incident light (including your laser light), hence its black appearance. On the other hand, your transparent glass sample is transparent because it is largely free from absorbing impurities, so the ambient and laser light is transmitted. Does that answer your question?
Thanks Jose and Eric. Now. I want to take this discussion into a bit more deeper. As the laser light moves inside the material which is doped by absorbing color dopants, it interacts with them but when the dopants are absent it gets transmitted. What happens when a laser light (say of 1 micron wavelength) interacts with the lattice or structures of transparent material.