Clean rooms are special environments designed to have less contaminants in the air than you find in everyday life. In some cases much less. Clean rooms are used for a variety of purposes most notably scientific research and engineering in the fields of biology and microelectronics. I'm most familiar with the latter and will focus on that (if anyone has experience with bio clean rooms please chime in in the comments).

a biotech clean room

Clean rooms are rated based on the amount of particles in a given volume of air. In everyday life you will find ~1,000,000 particles, .5um in diameter or larger, in every cubic foot of air. A class 10 clean room will have 10 particles, .5um in diameter or larger, in every cubic foot. A class 1 clean room will have just 1 in that same volume.

How big is .5um? A typical human hair is 70 microns in diameter.

Scanning electron microscope image of human hair

To give another example a surgical operating room rates as approximately a class 10,000 clean room. At my work we have to use class 1 and 10 clean rooms. So our working environment is 1000-10,000 times cleaner than where they cut people open.

To keep a clean room this, well, clean requires a great deal of effort. Air going into the clean room needs to be filtered as much as possible. The clean room itself is isolated into areas that are more or less clean, providing stages that items and people can go through.

An example of a clean room facility lay out. Blue areas are class 100, Yellow areas are class 10, and pink areas are service areas (dirtier). Click on the picture to go to the site where the map is interactive.

In the example above people will likely first go through pre-gowning before entering the actual gown room. Once gowned up they can enter the class 100 clean room (blue), then they can pass into the class 10 clean room (yellow) beyond. Designing the cleanliness in stages like helps considerably. Trying to keep the whole area at class 0 would require a lot of essentially wasted effort. Similarly the process tools (which can be pretty dirty on this scale) are kept in the service chases (pink areas) with just a front face open to the actual clean bays (blue and yellow areas). Again this segregation helps to maintain the pristine environment of the clean room.

The biggest threat to the clean environment once built is of course people. We constantly shed skin, we breathe out all kinds of crap. We sweat, we have dander, and on and on. Consequently you have the bunny suit:

Man in bunny suit gets "airshower" to blow off any particles before entering clean room

The bunny suit above is made of a material called Goretex.

SEM image of Goretex

The suit is designed not to allow water vapor to pass through and only limited oxygen flow. The suit above is not completely sealed, the face mask is open allowing air to enter the suit for respiration. To keep any exhaled materials from passing out of the suit the item on the man's lower back is a small vacuum pump. This is connected to the back of the helmet so that the suit is kept at lower pressure than the outside. Consequently airflow is always in through the front of the helmet. This kind of suit is appropriate to a class 1 clean room. For a class 10 you might see something more like this:

Bunny suits with simple hood

The suit is still made of goretex, the main difference is, instead of a helmet and vacuum system, you have a simple hood. Note the guys in this picture should not have their mouths exposed the way they do if this is a class 10 clean room. The hood is there to catch exhaled particles.

Typical gowning will go something like this:
PREGOWN (usually done outside of the gowning room)
1) drink water (helps limit the amount of particles you exhale by trapping them in solution)
2) pregown gloves/liner gloves (nylon gloves worn during gowning and under latex or nitrile gloves later)
3) Hairnet/beardnet
4) shoe covers
GOWNING (done inside the gowning room)
5) Bunny suit
6) Helmet/hood
7) belt with blower and batter pack for hood
8) boots
9) safety goggles
10) Latex or nitrile gloves

The bunny suit and gowning above is suitable to a microelectronics environment, i.e. a place where people are a danger to the materials. They are not appropriate to some biotech environments; where the materials may be a danger to the people. See the first picture above for something more suitable to virology labs.

You have to assume particles will get into the clean room, of course, and so you have to have systems in place to isolate and remove them as efficiently as possible. One key idea is that of laminar airflow. Laminar flow means that a fluid moves together, the molecules or atoms taking parallel paths. This is extremely different than "turbulent" flow that you find at normal air pressure.

Humfrey Bogart, and an example of turbulent vs. laminar

Look at Humfrey's cigarette smoke. At first there is a thin stream. This stream of particles are all moving upwards together. That's laminar flow. Then there is a change and the smoke puffs outwards in different directions creating visible whorls and eddies. That's turbulent flow. Here's more info on turbulent vs. laminar.

Air typically moves turbulently. The problem with turbulent air in a clean room is it means a particle can end up anywhere. There's no way to predict its motion because turbulent flow is so chaotic. Laminar airflow, on the other hand, is quite predictable. Unlike Bogart's smoke we want the Laminar airflow in the clean room to start at the ceiling and end at the floor. To accomplish this you put blowers in the ceiling and vacuum intakes in the floor. This means the air tends to constantly stream in through the top of the clean room, straight down through the clean room, and out through the floor. Any particles caught in this laminar flow will tend to be deposited on the floor tiles where constant mopping (with giant swiffer like mops) can remove them.

an example of the extremely high tech tools used to keep a clean room clean

Hopefully this brief overview gives a little insight into how clean rooms operate.