Lots of misinformation in this thread.
Any time an individual transacts $10,000.01 or more in a day (sum or deposits OR sum of withdrawals) the bank is required to file a CTR. The CTR is used to detect money laundering, so the IRS is not going to care about you creating a CTR one time. There are thousands if not tens of thousands of CTRs filed every day, so no one is going to be calling you and asking where you got that money from. Now if you owned a convenience store and regularly deposited $5,000 cash per day for several years and then it suddenly increases to $15,000 every day, they would probably be interested in that.
A CTR only takes a few minutes to complete if you are a customer of the bank, since they already have all of your relevant information (ID, SSN, address, occupation). It does not necessarily require your physical presence since it can be filed up to, I believe, 25 days after the transaction. It will take much longer if you are a non-customer making a deposit into someone else's account since they don't have any of your information and will want to cover their bases.
At exactly $10,000 a CTR is not filed. However the bank may instead file a Suspicious Activity Report if they believe you are structuring your transactions to avoid incurring a CTR. If you walk up and say you are putting $11,000 cash into your account and then change your mind to avoid the CTR, the bank has to file a SAR. They may also do a SAR if they see that you deposited $5,500 on two consecutive days on an account that typically has very few cash transactions since it will look like you are structuring anyway.
Also a Monetary Instrument Log has to be filed if you purchase or cash cashier's checks or money orders from $3,000 to $10,000 inclusive. The point of all of these is to detect money laundering. No reports are required for checks, wires etc because those transactions are traceable. For laundering to actually work the source of the funds has to be untraceable at some point, which is where the cash comes in. Drug dealers/racketeers/etc aren't going to have people write them a check for the heroin they just bought.
The easiest way to put your money back in the bank is to simply walk in and make your deposit and mention to the teller that you took it out just in case emergency a while ago. Because they will definitely be wondering.
P.S. Your money is FDIC insured up to a minimum of $250k in all interest-bearing accounts combined at a single financial institution, and 100% insured in non interest-bearing demand accounts. If things got to the point where your bank failed and the FDIC could not cover the losses, the country would have way bigger problems and cash would not be worth the paper it's printed on anyway.