There are many ways and materials to make molds. Molds can also be made from existing objects. Regardless of the material, certain characteristics have to be respected in order to separate the mold from the plastic and for the mold to retain its integrity.
In order for a form to be successful, draft, undercuts, density, ratio, materials and even shape are terms that affect a mold. Let's take one at a time.
1) Draft - Is a term used to describe a slight taper on a surface. In this case the vertical taper allows the mold to come out of the formed plastic reasonably easy, the draft or taper is what lets a stack of Solo cups nest inside each other for example, then release easily when pulled apart. If those same cups had no draft angle, they would not nest at all. Draft built into a mold will allow your mold to release with ease, noted in the first drawing.
2) Undercuts - Are inward creases, holes or areas that go inward beyond vertical. The result is the mold will be locked inside the formed plastic and cannot be remove without damage to the plastic and or mold.
3) Density - A mold must withstand the pull of vacuum. Hollow molds, especially with the addition of heat, may collapse under suction depending on the material. A mold must be filled with a dense material to serve as scaffolding to retain its shape integrity under heat and vacuum.
4) Ratio - A general rule of thumb for vacuum forming is the mold should be no more than twice as high as it is wide. This ratio is only a baseline to start from. Every mold is different and exceptions can be learned through experience.
5) Materials - Woods, composites, high density foams, resins, plasters, clays, metals and even natural materials, such as sea shells, glass, rocks and other solid materials can be used for molds.
6) Shape - The ideal shape for vacuum forming is a dome. As you get further away from that shape it becomes more difficult as your molds become more complicated. Dull edges, radius corners, shallow depth, slippery materials are all good characteristics of a successful mold.
In most cases it's best to use a 3D print as a master, shelving the print as a backup then making a fresh cast using the formed part. Casting is often faster to duplicate molds and non printed materials are often easier to smooth out if print textures are not desirable. Resin or heat tolerant filler can be used to duplicate molds. The alternative is to simply reprint the mold when the print fails, each time learning how to better fortify the 3D print.
Another issue with 3D printed parts is they get sticky. Not to the touch, rather plastic to plastic. When forming complex molds, plastic has to slide over corners and dip into voids. 3D print surfaces can soften slightly when being draped with hot plastic. Just enough so it causes some resistance (sticky). The result is the forming plastic does not slide freely over the printed mold, it grabs and stretches causing very thin spots and in some cases breaches (holes) losing vacuum needed to successfully form a quality part.
Choices must be made as to the versatility and durability for specific projects. One must consider the trade offs of more permanent materials that may be more difficult to alter but will last for many cycles vs. softer more workable material that is more easily altered however may not last for as many cycles.