Ten-millijoule, thirty-five femtosecond, 800 nm (~40 nm bandwidth) laser pulses are used to study high-order harmonic generation in helium- and neon-filled gas cells of various lengths. Harmonic orders in the range of 50 to 100 are investigated. A semi-infinite cell geometry produces brighter harmonics than cells of sub-centimeter length. In the semi-infinite geometry, the gas occupies the region from the focusing lens to a thin exit foil near the laser focus. Counter-propagating light is used to directly probe where the high harmonics are generated within the laser focus and to investigate phase matching. The phase matching under optimized harmonic generation conditions was found to be unexpectedly good with phase zones many millimeters long. Restricting the laser beam with an 8 mm aperture in front of the focusing lens increases the emission of most harmonic orders observed by as much as an order of magnitude. Optimal harmonic generation pressures were found to be about 55 torr in neon and 110 torr in helium. The optimal position of the laser focus was found to be a few millimeters inside the exit foil of the gas cell. Probing with counter-propagating light reveals that in the case of neon the harmonics are generated in the last few millimeters before the exit foil. In helium, the harmonics are produced over a longer distance. Direct measurement shows that the re-absorption limit for mid-range harmonics in neon has been reached.