It depends on how you distinguish your regular customers versus your wholesale customers. To modify your entire store to not accept any order below $100, what you could do is wrap this code around the submit button:
{% if cart.total_price >= 100 %}<div class="go-checkout"><input type="image" src="{{ 'button-check-out-now.jpg' | asset_url }}" value="Proceed to Checkout" name="checkout" /></div>
{% else %}<div class="go-checkout"><img src="{{ 'button-check-out-now-fade-new.jpg' | asset_url }}" border="0" /></div>
{% endif %}
BUT. This might not work if your store isn't dedicated in being a wholesale shop. Regular customers wouldn't be able to checkout because of this minimum order. If your store is half retail and half wholesale, please let me know how you identify wholesale customers from regular customers.