The quasi two-dimensional electron gas (2DEG) at the interface of two band insulators (LaAlO3 and SrTiO3) has very intriguing properties like high mobility, induced ferromagnetism and superconductivity. In this study, an industry compatible nano-patterning technique is developed, to pattern the LaAlO3/SrTiO3 interface down to 100 nm by using e-beam lithography and reactive ion etching (RIE). The process preserves the conductivity of interface, except a narrow depletion region. Moreover, in the nanostructures, the correlation between the interface conductivity and local structure of the SrTiO3 is studied. At low temperature structural phase transition of SrTiO3 leads to formation of domains within SrTiO3. These domains modulate the conductivity of the LaAlO3/SrTiO3 interface and the current is no more homogeneous within the domains, rather it flows in filaments at the boundaries of the domains and leaving the domain area basically insulating.