Second-harmonic generation microscopy (SHGM) has been employed to study crystals of zeolite-like material SAPO-5 filled with p-nitroaniline (PNA). The SHG and 2-photon fluorescence response of PNA in the one-dimensional channels readily reveals the pore accessibility; intergrown crystallites containing hexagonal pyramidal components and internal diffusion barriers are found next to seemingly perfect crystals. The sensitivity of second-harmonic generation to molecular orientation allowed for mapping of the domains of differently organized PNA. Dense domains of highly aligned PNA alternate with dilute zones with loosely aligned PNA.