You are right, we cannot see molecules directly
with our naked eye.
However, over the past few centuries, science has
developed a multitude of tools and theories that
shows us time and time again molecules and atoms
(their constituents) do exist. In fact, atoms have
had a fascinating history.
In the early days of the Greeks, Democritus
(along with several other philosophers) had a
thought experiment. He asked what would happen if
he kept dividing some material in half, eventually
he would come upon some piece that could no longer
be divided. This he called the "atom"
(which literally means indivisible).
Since then, many experimental techniques, in
combination with theoretical calculations, have
provided us an indirect way of measuring
properties of single molecules or atoms. For
example, molecules wiggle at specific frequencies
(i.e., the bonds between the atoms that compose
them fluctuate). You can shine light on these
molecules to measure these wiggles. Another
example is in biology, where you can tag a
molecule such as a protein or amino acid with a
fluorescent tag that make
pretty images . The previous link has those
We are also able to measure individual molecules
or atoms based on some other property such as
mass, charge, or magnetic moment. You can read
an example of it
here . Don't worry about understanding
everything; you'll learn many of the concepts as
you go through school.
Today we are at the point where we can
actually "see" individual atoms, and we can even
Most famously in scientific pop culture is
when IBM used a scanning tunneling microscope to move
individual Xe atoms to spell out IBM in 1989 .
Each of those
bumps in the picture corresponds to a Xe
It has been nearly thirty years since then, and
we've gotten even better at measuring atoms and
molecules. You can read more about it
Hope this helps!