Bis (trimethylsiloxy) silicon naphthalocyanine (SiNc) LB films were fabricated to align nematic liquid crystals. Films obtained under different surface pressures exhibit different alignment effects. Films obtained under surface pressure of 15mN/m will induce a planar alignment, while those obtained under 30mN/m will induce a homeotropic alignment. Atomic force microscopy reveals that on films prepared under high surface pressure the SiNc molecules stack into separate monomers or aggregates to form lines of nanometer size with molecular macrocycles perpendicular to the surface of the film and the dipping direction of its formation. In addition, there are grooves of molecular size between the stacked SiNc molecular lines. Similar formation occurs in films prepared under low surface pressures, only instead of molecules all lying perpendicular to the surface, many SiNc molecules are lying obliquely to the film surface or even lying on the surface. The mechanism of the liquid crystal alignment is also discussed.