Look at the relationship between a 2-D rendering (left, in a bond-line format) and the 3-D representation (right); you can (should) make this with your model kit.
Methane, the simplest hydrocarbon.
Octane has a longer chain of carbons.
Chloromethane, a haloalkane.
E-2-Butene, an alkene.
Dimethylacetylene or 2-butyne, an alkyne.
Trans-2-methylcyclohexanol, an alcohol.
Methylamine, an amine.
Acetophenone, a ketone. The ring is also a special structure, referred to as an "aromatic" ring.
Charged species: (These always exist in the presence of another, oppositely-charged ion to balance charge)
The methyleneiminium cation.
3-Hydroxypentanoate anion.
Multiple functional groups can appear in a molecule:
Morpholine has both an ether and an amine.
Morphine is a complex natural product with ether, amine, alcohol, and an aromatic ring.

You may also clear the 2-D structure (rectangle, second box on the top left) and draw your own molecule. Click the "-->" button to display a 3-D rendering.

There are different 3-D depictions of molecular structure. The "Ball & Stick" model that is the default on this page is kind of standard in that it distinguishes between the atoms as the cornerstone of the molecular framework, and the bonds that provide the force to hold them together. However, the problem is that this model fails to capture reality in terms of where things are: atomic nuclei are extremely small, and the electron cloud extends out quite a bit further than the model implies.

Alternatives include the "Wireframe" model, that emphasizes the atomic framework at the expense of "Where are the electrons?" and the Spacefilling model, that gives us a rough idea of the volumes encompassed by a large percentage of the electron density.