It has been demonstrated from recent research that modern uses of multiscale analysis, uncertainty quantification techniques, and validation experiments is essential for the design of nanodevices in biotechnology and medicine. The 3D immersed molecular electrokinetic finite element method (IMEFEM) will be presented for the modeling of micro fluidic electrokinetic assembly of nanowires, filaments and bio-molecules. This transformative bio-nanotechnology is being developed to enable gene delivery systems to achieve desired therapeutic effects and for the design and optimization of an electric field enabled nanotip DNA sensor. For the nanodiamond-based drug delivery device we will discuss the multiscale analysis, quantum and molecular mechanics, immersed molecular finite element and meshfree methods, uncertainty quantification, and validation experiments. In addition, we will describe the mathematical formulation of pH control interactions among chemically functionalized nanodiamonds, and their interactions with polymers. For the nanotip sensor, we will discuss the underlying mechanics and physical parameters influencing the bio-sensing efficiency, such as the threshold of applied electric field, biomolecule deformation, and nanoscale Brownian motion. Through multiscale analysis, we provide guidelines for nanodevice design, including fundamental mechanisms driving the system performance and optimization of distinct parameters.