The pretreatment of a high lignin substrate, coconut coir dust, was studied by chemical techniques (NaOH solution, ionic liquid, and NaOH followed by ionic liquid) and by a physical method (subcritical water, SCW). Following substrate pretreatment and a washing step, structural analyses were performed by scanning electron microscopy, X-ray diffraction (XRD), and Fourier transform infrared spectroscopy. It was found that all substrates pretreated by chemical methods had more amorphous structures than the untreated substrate. The XRD patterns of the chemically treated substrates shifted toward higher angles by 0.50° to 1.00°. However, the XRD peak symmetry of the SCW-treated substrate did not shift, but its crystallinity index decreased. The results revealed that lignocellulose treated with NaOH followed by ionic liquid at 120 °C for 30 min showed the greatest extent of structural transformation.