The importance of spatial location of nanoparticles in polymer nanocomposite materials has fueled interest in using block copolymers (BCP) as particle guiding scaffolds. Researchers have tailored the surface chemistry of functional nanoparticles (NPs) to prevent aggregates and selectively place them in desired BCP domains. However, magnetite NPs, having numerous potential applications in electrical and biomedical fields, tend to aggregate and phase separate from BCP matrix due to strong magnetic dipole attractions. To control the distribution and location of magnetic nanoparticles in a polymer matrix, we have used electrospinning (a process that draws polymer solution jets in the presence of electric field to form nanofibers) as a template to selectively place monodisperse magnetite NPs (~ 4 nm) in block copolymer nanofibers. When 4 wt% magnetite NPs coated with oleic acid are added to symmetric polystyrene-b-polyisoprene (PS-b-PI), transmission electron microscopy (TEM) images of microtomed, electrospun fibers reveal that NPs are uniformly dispersed only in the PI domain and the confined assembly of well-ordered alternate concentric rings of PS and PI domains is preserved. For 10-15 wt% NPs, a transition of morphology is seen from concentric rings to a bicontinuous phase with NPs again uniformly dispersed in the PI domain. To further understand the effect of flow conditions on the nanoparticle location in block copolymers, we have performed coarse grained molecular dynamics simulations using dissipative particle dynamics (DPD) thermostat under simple shear flow. First, we study the effect of shear on location of nanoparticles in block copolymers mimicking experimental systems where simple metal particles are coated with the desired block. Then we model the system, such that particle-particle interactions exceed those of particle-polymer, qualitatively resembling the PS-b-PI system with magnetite nanoparticles. From our results, we find that shear can play an important role in controlling the location of nanoparticles in block copolymer matrices.