This paper presents the effect of nanoscale damage layer on magnetic results obtained from the optimization of media overcoat deposition parameters on the top magnetic layer on magnetic hard disks. We have investigated the effects of interface interaction between the overcoat deposition parameters on the top magnetic layer on the media by using a plasma enhanced chemical vapor deposition (PECVD) on next generation hard disks. The goal is to achieve a reduced damage layer, lower head media spacing (HMS) and a higher spectrum of signal to noise ratio (SpSNR) optimized by using Taguchi experimental design with a four-factor three-level (L9) orthogonal array. An analysis of variance (ANOVA) was carried out to interpret the measured coercivity (Hc), HMS and SpSNR. It was found that source gas type is the most significant factor with a percentage contribution effect of 59.8% on HMS and 51.7% on SpSNR. The bias voltage is the second most significant factor with its percentage contribution being 24.2% on HMS and 31.0% on SpSNR. Overall, the optimum SpSNR was obtained using a C2H2 source gas, −100 V bias voltage, 50 V anode voltage and 20 sccm gas flow rate, respectively.