I didn't think you could place single pads in PCBNew . . . . but, if you did, you should be able to delete them like any other item: select it, then either the "DEL" key, or right-click and select "Delete".
Same thing is true if you placed a footprint that included only a single pad: select it, then "DEL".
It's probably much easier to select a block of pads, then delete the entire block. Make sure you have block-selected ONLY the pads you want to remove!
If you placed the pad as part of a multi-pad footprint you must delete the entire footprint.
With any of these methods, the pad will be removed from all of the layers it affects.
Now, please tell us a few things about your project.
Your plot shows A LOT of pads with no connections. Are you CERTAIN that components won't be mounted on those pads?
On a commercially fabricated circuit board, "pads" and "vias" are essentially the same physical construction. That's why we can use pads to do "via stitching". Why do you think pads are preferable to vias " to connect top and bottom layer where ever needed" on your board?