I would not classify Freemasonry as a secret society. Freemasonry wants new members and while recruiting is (supposed to be) a big no-no, being visible (preferably while bettering your community) is encouraged.
The appearance of symbols in movies and other media are somewhat like rickrolling or "masons were here" tagging, intended for other masons. An allusion to the "We Are Everywhere" motto which is intended well, but ends up sounding ominous to outsiders.
There are appendant bodies within Freemasonry that certainly are secret societies. Even secret from most Masons. Some Googleable (eg. J-----rs), some not. I can answer more specific questions here, if desired.
They have their own legends, symbols, and modes of recognition. Some of these are as small as a few people, and some are worldwide.
Source: Am one.
Edit: I should mention that this is all from my perspective in the US. European Freemasonry works substantially differently and I'm not familiar with perceptions and processes there. Thanks cm2187