DNA sequencing is an essential process for determining the nucleotides on a DNA strands and this process is of high importance in medicine and biomedical research. Nanopore based DNA sequencing has been widely researched and analyzed during last years and this is very important to improve all parameters involved in the process of DNA translocating through these nanopours. Ionic current resolution is a key parameter in designing these nanopours for better measuring of this infinitesimal current that is in order of nano A or even pico A. Here by means of molecular dynamics simulation we showed that using fluorinated carbon nanotubes while embedded inside silicon membrane results a higher ionic current compared to pristine carbon nanotubes. We simulated pristine carbon nanotubes (PCNT) and fluorinated carbon nanotubes (FCNT) with chirality of (8,8) and (10,10) which corresponds to diameter of 1.07 nm and 1.34 nm respectively. Ionic current analysis of these inorganic nanopours functionalized with carbon nanomaterials showed that it could double or triple the magnitude of ionic current. For FCNT (8,8) the magnitude of ionic current was 1.984 nA while it was 0.891 nA for PCNT (8,8) embedded in silicon nanopore. Our study introduces the fluorination of carbon nanotubes as potential method for designing high resolution DNA sequencing nanopore devices.