Mesoporous material MCM-41 with uniform hexagonally ordered pores in range of 2-10 nm was synthesized through hydrothermal method. The synthesis started from highly pure silica source known as Ludox which act as an active source of silica in the presence of organic surfactant (CTABr) as structure-directing agent. MCM-41 has been functionalized with the organic group known as 3-aminopropyltriethoxysilane (APTES), 3-mercaptopropyltrimethoxysilane (MPTMS), and chloropropyltriethoxysilane (CPTES) by co-condensation method in order to enhance the surface hydrophobicity of MCM-41. The increasing hydrophobicity will lead to efficient reaction specifically for organic reaction in organic solvent. The resulting materials were characterized with various techniques which are PXRD, FTIR, NMR, Elemental Analysis and AAS. The formation of uniform hexagonal framework of synthesized materials was shown in PXRD result. The functionalized groups of modified MCM-41 can be characteried via FTIR and 13C-NMR results. The Elemental Analysis shows the percentage of nitrogen, carbon, hydrogen and sulphur in MCM-41 and functionalized MCM-41. From AAS, MCM-41 MPTMS has high capability for removal of Cu (II) in aqueous solution compared with others.