The development of efficient biomolecular separation and purification techniques is of critical importance in modern genomics, proteomics, and biosensing areas, primarily due to the fact that most biosamples are mixtures of high diversity and complexity. Most of the existent techniques lack the capability to rapidly and selectively separate and concentrate specific target proteins from a complex biosample, and are difficult to integrate with lab-on-a-chip sensing devices. The development of an on-chip silicon nanowire filtering, selective separation, desalting, pre-concentration, and controlled release platform for the direct analysis of whole blood and other complex biosamples, will be described. The separation of required protein analytes from raw biosamples is firstly performed using an antibody-modified roughness-controlled silicon nanowire forest of an ultra-large binding surface area, followed by the fast release of target proteins in a controlled liquid media, using drastic pH change near silicon nanowire surface. The pH change caused by illumination of photo-acid/photo-base which covalently bonded to nanowires surface. Importantly, this is the first demonstration of 3D nanowire on-chip filter with ultra-large binding surface area and reversible light-controlled release of adsorbed analyte molecules for direct purification of blood samples, able to selectively collect and separate specific low abundant proteins, while easily removing unwanted blood components (proteins, cells) and achieving desalting effects, without the requirement of time-consuming centrifugation steps, the use of desalting or affinity columns. Furthermore, this 3D nanowire light controlled filter separation device can be easily integrated into a single platform with downstream silicon nanowire-based sensors arrays, which successfully applied for the multiplex, real-time and ultrasensitive detection of biomarkers.