how to filter out cell after doing QC
Yes, you end up placing filters where things become inconsistent or similar to background. In the example, which appears to be from the Seurat tutorial, there's a downward plunge in nGenes vs. nUMI at around 200 genes and few believable cells with more than 2000-2500 genes, so the tutorials sets filters around there. The 0.05 mitochondrial contamination is a more arbitrary round number and is less supported by the plots (one would use more like 0.06 or 0.07 if one based this solely on the plots).