Point-of-care virus diagnosis is highly desirable in worldwide infectious disease control. Here we report a hand-held device for capturing viruses by applying physical size based exclusion inside a point-of-care device integrated with vertically aligned carbon nanotube (VACNT) nanostructures to achieve label-free and high throughput virus capture. The microfluidic device is constructed from a VACNT channel wall synthesized bottom-up via chemical vapor deposition (CVD). The VACNT has ~117nm average gap size and ~97% porosity. By bonding with a polydimethylsiloxane (PDMS) cover sealing the top, the aqueous sample containing virus particles filter through the VACNT channel wall under negative pressure applied at the outlet end. We have demonstrated that the device is capable of filtering 50µL of PBS containing ~6.3×104 counts of lentivirus particles in 10 minutes with 97% of capture efficiency, quantified by the cell infectious titration technique.