You can filter them out by setting a custom parameter on the _index.md
of these sections.
Something like this would do. (This is in YAML you can figure out the TOML)
exclude: true
And then simply place the following in the relevant template to exclude these sections from your navigation.
{{ $sections := .Site.GetPage "section" .Section }} {{ range where $sections "Params.exclude" "ne" "true" }}
EDIT
I changed the above snippet because what I posted originally is meant for Nested Sections.