Eu não uso htop, mas a julgar pela página de manual , parece que você pode usar o espaço bar para "marcar" um processo, então a função F9 / k kill será aplicada somente a esse processo.
Space
Tag or untag a process. Commands that can operate on multiple processes, like "kill", will then apply over the list of tagged processes, instead of the currently highlighted one.
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F9, k
"Kill" process: sends a signal which is selected in a menu, to one or a group of processes. If processes were tagged, sends the signal to all tagged processes. If none is tagged, sends to the currently selected process.