The helium ion gas field ion source is a novel charged particle source technology with potentially greater capabilities than electron beam based tools for imaging and nanomachining [Ward , J. Vac. Sci. Technol. B (to be published); Morgan , Microscopy Today 14, 24 (2006); V. N. Tondare, J. Vac. Sci. Technol. A 23, 1498 (2005)]. Potential strengths of He ions over electrons (scanning electron microscopy) are improved thin film surface sensitivity, material contrast, IBIC voltage contrast, Rutherford backscattering material contrast, and the ability to utilize in situ electron charge neutralization on floating substrates which have enhanced charging properties (e.g., masks, photoresist). In this article, the authors will discuss and illustrate examples highlighting several of these attributes. Helium ions, unlike electrons, induce collision events in the material lattice. A critical area to understand is the operating conditions and sample types for which the advantages of helium ion imaging can be realized. Dose, beam current, acceleration voltage, and material interaction are all key areas for modeling and empirical analysis to determine potential invasiveness. The focus of the study presented in this article relates to analyzing the potential lattice damage induced in silicon substrate for ion doses ranging from 1x10(14) to 5x10(15) ions/cm(2). This range represents relatively light dose (fast scan) to intermediate dose (slow scan) imaging applications. Findings for doses in this range (as typically used in image applications) show little to no damage to the silicon lattice. This finding also agrees with SRIM [Ziegler et al., The Stopping and Ranges of Ions in Solids (Pergamon, New York, 1985), Vol. 1] Monte Carlo simulations, which predict that helium ion induced defect densities to be 4x10(17) to 4x10(18) dis/cm(3). However, it is clear that with higher doses, defect densities will increase to a level that may be invasive to device structures (e.g., metal oxide semiconductor field effect transistor channels or gate oxides). (C) 2007 American Vacuum Society.