High harmonic spectroscopy relies on high harmonic generation (HHG) in aligned molecules. The first step of HHG is the ionization of the molecule in the intense femtosecond laser field.Here we present measurements of both ionization yield and high harmonic yield as a function of molecular angle in N 2 and CO 2 molecules. Measurements were done at two wavelengths, 800 and 1200nm, and for a range of laser intensities, to study the sensitivity of laser conditions on both processes. The behavior of N 2 was relatively insensitive to laser conditions. However in CO 2 , a minimum in high harmonic emission was observed that was sensitive to both laser intensity and wavelength, and was attributed to interference in emission from the HOMO and HOMO-2 orbitals.