It is rather difficult to differentiate between the two with the naked eye. However, you can use a microscope to observe the two. Natural Ruby will have pits, cracks, and fissures that can be very easily visible whereas glass filled Ruby will have these cracks, pits, and fissures filled with lead glass, which would appear in the form of transparent glass. One can also compare the transparency of both these gemstones in order to differentiate between them. Natural Ruby will have visible inclusions whereas glass filled Ruby would be transparent.
However, we advise that you consult a gemstone laboratory to differentiate between a glass filled Ruby and a natural Ruby. These labs make use of modern technology and skilled gemologists that test and verify these gemstones. Upon doing this, they issue a lab certificate mentioning the necessary details about the gemstone.
At GemPundit, you can find a wide collection of glass filled Rubies certified and verified by renowned gemstone testing labs such as AGR, JBN, GEMTRUE, ITLGJ, and ISKON.