Hi ravi_litb,
varuniyengar is totally right when saying the thickness defines the operating frequency. Just to clarify a bit more (hope this is not redundant). When you go higher in frequencies you can see unwanted modes propagating through your substrate if too thick.
The choice of the thickness is a deal between operating frequency, size of the structures your can at the end manufacture (closely related to ε too) and tolerances you can live with.
Attached a small image from Microwave101 showing a rule of thumb to choose the substrate thickness.
**broken link removed**