One of the most common methods for chocolatiers to make their own molds is to use food grade, liquid silicone rubber. The problem is that liquid silicone rubber is very expensive and can take a long time to set. If your silicone inadvertently gets air in it while mixing or pouring, you may very well go through the whole process only to find that your mold did not turn out right because of one unsightly placed air bubble.
There are several things that can be done. The simplest form is not over-mixing and brushing a small layer of the silicone on the model before pouring the whole mold. This way you get into the detail and have less air bubbles on the surface where it matters most. The next best thing you can do is use a vacuum degasser. To use a vacuum degasser, the mixed liquid silicone is put in a chamber before it is poured. This process will break up most of the air bubbles before casting. This is very effective, but not all the way as air can be brought back during the pouring.
The best way to ensure a bubble free mold is to use a pressure casting method. A pressure pot is a metal chamber that uses a compressor to cure the mold under pressure. The liquid silicone is poured over the model then placed in the chamber. The pressure, max 60 psi, eliminates the bubbles during the cure process. You can buy pressure pots at Smoot On, or I have seen them used for the paint industry which can be bought at many places, even Amazon (link will take you right to the pressure pots).
Word of caution: do not attempt to make your own pressure pot as they can explode.
To read more about mold making see our in depth instructions on The Chocolate Mold Factory's Main Site under "Personalized Molds". There are tutorials about designing molds and how to make them. Though the site is geared towards chocolate molds, these instructions are the same as would be for any other type of non food grade mold.