A sample preparation method is described for enabling direct correlation of site-specific plan-view and cross-sectional transmission electron microscopy (TEM) analysis of individual nanostructures by employing a dual-beam focused-ion beam (FIB) microscope. This technique is demonstrated using Si nanowires dispersed on a TEM sample support (lacey carbon or Si-nitride). Individual nanowires are first imaged in the plan-view orientation to identify a region of interest; in this case, impurity atoms distributed at crystalline defects that require further investigation in the cross-sectional orientation. Subsequently, the region of interest is capped with a series of ex situ and in situ deposited layers to protect the nanowire and facilitate site-specific lift-out and cross-sectioning using a dual-beam FIB microscope. The lift-out specimen is thinned to electron transparency with site-specific positioning to within ∼200 nm of a target position along the length of the nanowire. Using the described technique, it is possible to produce correlated plan-view and cross-sectional view lattice-resolved TEM images that enable a quasi-3D analysis of crystalline defect structures in a specific nanowire. While the current study is focused on nanowires, the procedure described herein is general for any electron-transparent sample and is broadly applicable for many nanostructures, such as nanowires, nanoparticles, patterned thin films, and devices.