They are loupe clean and free of inclusions. However, there is a grade above this when talking about diamonds. Diamonds can also be Flawless. So, what is the difference? A diamond graded as internally flawless shows no inclusions under 10x magnification, but there are blemishes on the surface. On the other hand, for a diamond to be considered flawless, a trained eye must not observe any inclusions or blemishes under a 10x magnification.
The easiest way to describe the difference in that Flawless diamonds show NO blemishes on the surface of the stone and no inclusions inside, meanwhile Internally Flawless diamonds have no inclusions, but do show blemishes on the surface. And that is why the grade receives the name Internally flawless, because the inside of the stone is perfect, but the outside shows some blemishes.
In regards, to colored gemstones, Internally Flawless is the top grade you can find, as finding a colored stone without blemishes is extremely rare. Even rarer than a flawless diamond. There are examples of flawless Emeralds, but their rarity means their price is significantly higher than any other type of emerald. Furthermore, darker colored stones such as garnet or blue topaz can have deeper inclusions because their depth of color is able to hide the flaws in the stone. Meanwhile, lighter colored stones have more trouble disguising flaws under a rich color.