How do I manually focus lenses with current DSLRs?

The viewfinder "focus" screen on modern cameras is optimized for brightness, not focus verification (the exception to this is the Nikon Df, which has a slightly better groundglass than other Nikon DSLRs. (By the way, you customers asked for it to be this way and the camera companies complied.) You have three choices: use Live View, especially with magnification; use the autofocus verification indication in the viewfinder; or get a focus-help screen like those sold by third party vendors.

I should note that with some cameras (e.g., D500, D8xx series, D4/D4s, and D5) you can use HDMI output to an external HDMI monitor for Live View and the output is good enough to give you a better look at what’s going on. This gives you a few potential gains: you can get a bigger than 3" screen (7" is typical these days, and you can get bigger), and many of these external HDMI monitors have focus peaking built in. Focus peaking is a method by which the display is highlighted in areas that are "in focus." 

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