Measure and control molecular internal structure plays a critical role in many applications such as molecular electronics and DNA sequencing. I will present the progress in exploring molecular internal structure of fullerenes, diamonoid, and DNA with two distinct instruments: scanning tunneling microscopy (STM) and nanopore. Our STM studies of C60 fullerene include observation of energy-resolved molecular orbitals, molecule-substrate interactions, and the Jahn-Teller effect. I will also present the studies of new sp3 bonded diamondoid molecules, including inelastic local spectroscopy, manipulation properties, and results from voltage-pulse modification. DNA is a very important biomolecule with genetic information coded in the sequence of its bases. The attempt to sequence DNA with STM had shown great difficulties and I will present the current status and the new schemes to detect DNA sequence based on nanopore devices.