Nonlinear optical nanoscale waveguides are a compact and powerful platform for efficient wavelength conversion. The free-standing waveguide geometry opens a range of applications in microscopy for local delivery of light, where in situ wavelength conversion helps to overcome various wavelength-dependent issues, such as biological tissue damage. In this paper, we present an original patterning method for high-precision fabrication of free-standing nanoscale waveguides based on lithium niobate, a material with a strong second-order nonlinearity and a broad transparency window covering the visible and mid-infrared wavelength ranges. The fabrication process combines electron-beam lithography with ion-beam enhanced etching and produces nanowaveguides with lengths from 5 to 50 μm, widths from 50 to 1000 nm and heights from 50 to 500 nm, each with a precision of few nanometers. The fabricated nanowaveguides are tested in an optical characterization experiment showing efficient second-harmonic generation.