Magnetic Resonance Force Microscopy (MRFM), also often described as nanoscale Magnetic Resonance Imaging (nanoMRI) is a imaging technique for visualizing the three-dimensional internal structure of spin-active samples on the sub-nanometer level. In practice, the sample in question is often a biological sample, and in the case of this thesis, a influenza virus. The sample is placed at the end of a long thin lever fabricated from monocrystalline silicon, called cantilever, and placed in close proximity to a micrometer-scale antenna with a nanoscale magnet placed on top, which is called a microstrip. With this specific setup, aspects of Nuclear Magnetic Resonance (NMR) and Atomic Force Microscopy (AFM) are combined to allow for the detection of minute spin forces emanating from the sample itself. Through the presence of a magnetic field gradient, specific regions in the sample called resonance slices may be selectively addressed and the force generated from this part of the sample is registered by the cantilever. By scanning the cantilever in relation to the microstrip, 2D and 3D images are recorded. From these images, the spin density of the sample and by extension its molecular structure can be recovered by means of a deconvolution algorithm. In previous work performed on our setup, its has been the goal to create a coherent 3D image of a influenza virus in order to demonstrate the system’s capabilities. During the course of the measurement series to do so, strong interactions between the cantilever and the nanomagnet placed on the microstrip were observed. These interactions caused the formation of physical gaps in the scanning grid of the cantilever on the order of 100 nm, meaning our force sensor could not be freely scanned over the nanomagnet without suffering significant displacement. We refer to these inaccessible regions as "blind spots", since no spin signal can be gathered from these regions. In addition, the cantilever resonance frequency would rise considerably in proximity to the nanomagnet, causing difficulty with the cantilever feedback and consequently with signal processing. Considerable advances in terms of feedback stability were made, but the issue of blind spots and frequency spikes persisted. The main goal of this thesis was to develop a solution for this phenomenon. The solution was sought in the form of a new generation of microstrip with a new geometric configuration of the antenna and nanomagnet: instead of a stacked design with the nanomagnet sitting on top of the antenna, a planar, embedded design with the nanomagnet embedded inside the antenna was developed. The development of this new microstrip generation necessitated a complete reinvention of the fabrication process over the course of three years; the new fabrication process uses Ion Milling to physically carve nanomagnets from a thin Iron-Cobalt (FeCo) alloy film through the use of a dielectric hard mask, places a gold film over the entire assembly and subsequently uses glancing angle ion milling to planarize the gold film and bring its surface to a flush connection with the nanomagnet edges, resulting in a flat surface of gold with nanomagnets seamlessly embedded in it. This design was successfully introduced into the MRFM setup and demonstrated superior characteristics in terms of blind spot generation and resonance frequency spikes. In addition, the Ion Milling-based fabrication process resulted in nanomagnets with a significantly higher magnetic field gradient, registering an increase by a factor of 3.75 when compared to previous designs. The measurements conducted with the new device generation demonstrated superior signal strength and the ability to record viable datasets with considerably shortened measurement time, which is a major Achilles heel of MRFM.