The large size of amylopectin represents an experimental challenge for standard analytical techniques to characterize its structure at the molecular level in dilute solution. We introduce a methodology that combines pyrene excimer fluorescence (PEF), the fluorescence blob model (FBM), molecular mechanics optimizations (MMOs), and intrinsic viscosity ([η]) to probe the interior of complex macromolecules with a heterogeneous interior like amylopectin. The combination of PEF, FBM, and MMOs yields the density (ρ fluo ) of nanosized subvolumes of the macromolecule, called blobs within the framework of the FBM, while [η] yields the density (ρ) probed over the length scale of the entire macromolecule. Comparison of ρ and ρ fluo indicates whether matter is either homogeneously (ρ = ρ fluo ) or heterogeneously (ρ < ρ fluo ) distributed inside the macromolecule. The main advantage of the methodology is to shift the focus of the study from the entire polydisperse macromolecule to that of monodisperse blobs where a blob represents the volume probed by a given pyrene derivative. This methodology is thus ideally suited to probe polydisperse heterogeneous macromolecules in solution. It is applied to amylopectin. The finding that ρ was much smaller than ρ fluo for amylopectin in dilute solution led to the conclusion that the side chains of amylopectin are heterogeneously distributed inside the amylopectin interior. The ρ fluo value agreed with the notion that the helical side chains of amylopectin form clusters where the side chains are ∼2.7 nm apart. When ρ and ρ fluo were determined for nanosized amylopectin fragments (NAFs) produced through extrusion, ρ fluo took the same value as for amylopectin while ρ increased with decreasing NAF size, approaching ρ fluo for the smallest NAF. This observation led to the conclusion that the clusters of helical oligosaccharide side chains were loosely connected to each other via linear oligosaccharide segments. These features were captured by the solution-cluster (Sol-CL) model which seems to rationalize many of the experimental observations made about amylopectin.