Ultra-short laser pulses possess many advantages for materials processing. Ultrafast laser has a significantly low thermal effect on the areas surrounding the focal point; therefore, it is a promising tool for micro- and submicro-sized precision processing. In addition, the nonlinear multiphoton absorption phenomenon of focused ultra-short pulses provides a promising method for the fabrication of various structures on transparent material, such as glass and transparent polymers. A laser direct writing process was applied in the fabrication of high-performance three-dimensional (3D) structured multilayer microsupercapacitors (MSCs) on polymer substrates exhibiting a peak specific capacitance of 42.6 mF·cm^–2 at a current density of 0.1 mA·cm^–2. Furthermore, a flexible smart sensor array on a polymer substrate was fabricated for multi-flavor detection. Different surface treatments such as gold plating, reducedgraphene oxide (rGO) coating, and polyaniline (PANI) coating were accomplished for different measurement units. By applying principal component analysis (PCA), this sensing system showed a promising result for flavor detection. In addition, two-dimensional (2D) periodic metal nanostructures inside 3D glass microfluidic channels were developed by all-femtosecond-laser processing for real-time surfaceenhanced Raman spectroscopy (SERS). The processing mechanisms included laser ablation, laser reduction, and laser-induced surface nano-engineering. These works demonstrate the attractive potential of ultra-short pulsed laser for surface precision manufacturing.