Some stones out in the market can be tricky to tell the difference between either genuine or synthetic. In most cases, you will need much more than just a well trained eye.  Sometimes it may call upon some higher tech equipment to tell you the difference. 

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There are times when you may cross a gemstone that may look legit, but turns out to be expensive glass, Cubic Zirconia (CZ), or a different stone sold under a different name.  Some of the ways that you can tell if it's a fake is by inclusions; but not 100% of the time will that work.  Some cases you'll need a Microscope, a Refractometer, Chelsea Filter to help do the job,  

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Image above shows the difference between a genuine Diamond gemstone to those of synthetics.  Synthetics are sometimes intentionally used as a Diamond substitute..

 

For instance, natural Quartz up close will show veil-like inclusions inside a crystal, while synthetic stones often have air bubbles as inclusions.  Keep in mind that also colors can be copied just like the natural counterparts.  If you set a faceted purple glass stone and a natural deep purple Amethyst of the same color next to each other, it would be a little tricky to tell which is what on the spot.

 

A loupe can only do so much for when you are checking out a stone up close.  True it will show you inclusions inside a stone, but sometimes this is where you'll need more tools to help you identify a stone. 

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Knowing the terminology between naturals, simulated, synthetic, and composites is crucial.  When one thinks simulated, they think it's completely fake.  To help clear this up, synthetic is used for "fake" or "imitation" gems, such as cubic zirconia, YAG, GGG, or plastics.  Since there is no real natural counterpart in nature to these particular gemstones.  Simulated refers to be a real gemstone, but instead of growing in the earth, it was grown in a lab.  Same identical chemical compositions and crystal structures, just grown in a simulated environment.  Natural refers to what it sounds like; grown from within the earth's crust.  Natural should only be referred to stones that has a natural origin of creation (think earth grown). 

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*Don't think glass is just an imitation, there is a natural variety of glass known as obsidian (volcanic glass) and moldavite (caused by extra terrestrial impacts such as meteorites) both are a form of silicate.