A significant and largely unsolved problem of computational fluid dynamics (CFD) simulation of flow in anatomically relevant geometries is that very few calculated pathlines pass through regions of complex flow. This in turn limits the ability of CFD-based simulations of imaging techniques (such as MRI) to correctly predict in vivo performance. In this work, I present two methods designed to overcome this filling problem, firstly, by releasing additional particles from areas of the flow inlet that lead directly to the complex flow region (“preferential seeding”) and, secondly, by tracking particles both “downstream” and “upstream” from seed points within the complex flow region itself. I use the human carotid bifurcation as an example of complex blood flow that is of great clinical interest. Both idealized and healthy volunteer geometries are investigated. With uniform seeding in the inlet plane (in the common carotid artery (CCA)) of an idealized bifurcation geometry, approximately half the particles passed through the internal carotid artery (ICA) and half through the external carotid artery. However, of those particles entering the ICA, only 16% passed directly through the carotid bulb region. Preferential seeding from selected regions of the CCA was able to increase this figure to 47%. In the second method, seeding of particles within the carotid bulb region itself led to a very high proportion (97%) of pathlines running from CCA to ICA. Seeding of particles in the bulb plane of three healthy volunteer carotid bifurcation geometries led to much better filling of the bulb regions than by particles seeded at the inlet alone. In all cases, visualization of the origin and behavior of recirculating particles led to useful insights into the complex flow patterns. Both seeding methods produced significant improvements in filling the carotid bulb region with particle tracks compared with uniform seeding at the inlet and led to an improved understanding of the complex flow patterns. The methods described may be combined and are generally applicable to CFD studies of fluid and gas flow and are, therefore, of relevance in hemodynamics, respiratory mechanics, and medical imaging science.