Ion beams have been used to modify surface topography, producing nanometer-scale modulations (and even subnanometer ripples in this work) that have potential uses ranging from designing self-assembly structures, to controlling stiction of micromachined surfaces, to providing imprint templates for patterned media. Modern computer-controlled Focused Ion Beam tools enable alternating submicron patterned zones of such ion-eroded surfaces, as well as dramatically increasing the rate of ion beam processing. The DualBeam FIB/SEM also expedites process development while minimizing the use of materials that may be precious (Diamond) and/or produce hazardous byproducts (Beryllium). A FIB engineer can prototype a 3-by-3-by-3 matrix of variables in tens of minutes and consume as little as zeptoliters of material; whereas traditional ion beam processing would require tens of days and tens of precious wafers. Saturation wavelengths have been reported for ripples on materials such as single crystal silicon or diamond (∼200nm); however this work achieves wavelengths >400nm on natural diamond. Conversely, Be can provide a stable and ordered 2-dimensional array of <40nm periodicity. Also ripples <0.4nm are fabricated on carbon-base surfaces, and these quantized picostructures are measured by HR-TEM and electron diffraction. Rippling is a function of material, ion beam, and angle; but is also controlled by chemical environment, redeposition, and aspect ratio. Ideally a material has a constant yield (atoms sputtered off per incident ion); however, pragmatic FIB processes, coupled with the direct metrological feedback in a DualBeam tool, reveal etch rates do not remain constant for nanometer-scale processing. Control of rippling requires controlled metrology, and robust software tools are developed to enhance metrology. In situ monitoring of the influence of aspect ratio and redeposition at the micron scale correlates to the rippling fundamentals that occur at the nanometer scale and are controlled by the boundary conditions of FIB processing.