The effects of synthesis parameters (i.e. [TEOS], [TPA(+)], [OH-] and dilution) on membrane surface morphology is investigated for zeolite membranes grown on seeded supports (i.e. porous glass and alumina). Microstructural parameters including crystal size (d) and shape (M), apparent surface porosity (R-a) and average grain boundary (G) are used to quantify the membrane surface morphology. An empirical model that relates the length (l) and width (w) of the grain facets to the synthesis variables is derived based on the experimental data. The model gives an adequate description of membrane surface morphology and provides guidance for the synthesis of zeolite membranes with engineered microstructure. Helium, argon and sulfur hexaflouride gases are used as molecular probes to investigate zeolite membranes with different grain sizes (i.e. 0.6-1.1 mum) and grain morphologies (width-to-length ratio, M = 0.15-0.95). The single gas permeation experiments demonstrate that micro-scale structural property, such as zeolite grain size and morphology can affect the transport properties of the membrane. This work represents an initial step towards the rational design of engineered zeolite membranes for separation applications.