A relatively simple and inexpensive micromachined arrayed thermal probe apparatus, system for thermal scanning a sample in a contact mode and cantilevered reference probe for use therein can be used for a variety of microscopy and microcalorimetry applications ranging from the monitoring of processes in semiconductor manufacturing to the characterization of nano-scale materials, imaging of biological cells, and even data storage. Probes are designed to have very high thermal isolation and high mechanical compliance, providing advantages in both performance and ease of operation. In particular, an array of probes can be used for high throughput contact mode scanning of soft samples without mechanical feedback, and can, therefore, be used in wide arrays for high-speed measurements over large sample surfaces. The probes are preferably manufactured by a photolithographic fabrication process, which permits large numbers of probes to be made in a uniform and reproducible manner at low cost.