There is a few things you can do, and its also your own choice in which order (if any) you follow this in:
if its one user or two users, you may wanna consider using options a or c.
a) You can type /mode yournick +c
Consider this a " soft " layer of defense(50%), it stops any messages from users who are not in the same rooms as you, this is very easy to avoid and bypass but often one of the best ways to stop a flood or even people bothering you.
b) you can use /mode yournick +R
Consider this a much harder layer of defense (75%), it stops any Unregistered nicknames from sending you pvts and notices, floods from users still may bypass this setting though as they can be registered unlike flood bots.
You can use /silence +nickname
this is mainly for if there is a few users bothering you that you don't wish to talk too.
You can use /silence +*!*@*.*.*.*
Consider this as the Absolute protection (100%), this command will stop EVERYONE (except the chanops, ophelpers, botops & ircops + the bots in the mains room) from sending you pvts and notices.
When you feel comfy about removing these settings simply use the same command but change the + to a - and that will remove the setting used.
** note: yournick means your nickname on irc at the moment in time, if it bootstrap then the commands would be /mode bootstrap +R etc **