So I'm working on a Sorcerer who pretends to be non-magical to swindle people. His arcane focus is a cane he uses.

Casting subtle spell meta magic removes the Verbal and Somatic parts of a spell, but it implies that the Components cost remains.

My question is: Would I have to do anything with my cane focus when I cast a spell with subtle spell? I know I have to be holding my focus, but with no Somatic parts, wouldn't I just be able to hold it and not wave it around or anything?

Also, I'm sure my focus would glow or something as I channel magic through it, I'm just asking about movent and how obvious my spellcasting would be using it with subtle spell.

You rightly point out that subtle spell removes somatic and verbal components. The other relevant rules come from the Components rules and the Xanathar's section on perceiving a caster at work. The component rules say:

A spellcaster must have a hand free to access a spell’s material components — or to hold a spellcasting focus — but it can be the same hand that he or she uses to perform somatic components.

Which gives little indication about how much the material component is involved. On the other hand, there is an optional rule in Xanathars that states:

...To be perceptible, the casting of a spell must involve a verbal, somatic, or material component. The form of a material component doesn’t matter for the purposes of perception, whether it’s an object specified in the spell’s description, a component pouch, or a spellcasting focus.

If the need for a spell’s components has been removed by a special ability, such as the sorcerer’s Subtle Spell feature or the Innate Spellcasting trait possessed by many creatures, the casting of the spell is imperceptible. ...

So it seems that Xanathar's indicates that whatever you have to do with your cane is noticeable by others trying to perceive a caster, since the material component isn't removed by Subtle Spell. Whether that is glowing or hand movements or what is going to be between you and your DM.

This is a question for your DM, waving your focus around would be a somantic component but the rules are sient about whether a focus changes is any perceptable way when you cast a spell (like glowing)

When I DM and the DM of the games I am in as a player rule that there is nothing  perceptable happens when a spell is cast subtley but for your game you will need ot ask your DM.

If you cast a spell with costless material component and Subtle metamagic, you must have a hand free to hold your cane. 

The DM will tell if anyone notice your spellcasting this way.

Thanks, that does clear things up for me. I'll see what my DM says about it.

I Do think the other users have valid points: it may be much more difficult to notice and definitely needs a talk with the DM.