There is absolutely nothing you can do to make sure that your system is entirely clean, unless you also had experience with firmware (e.g. flashing of the BIOS) and hardware (e.g. changing hardware components). You see, stepping aside from malware infections which can be obtained through your computer usage, malware can be pre-installed on the system... It's been seen in the past and been linked to government agencies, Kaspersky identified such things awhile back. There are also similar cases where adware has been packaged with systems from manufacturer companies.
As a user though, and since I do know you weren't referring to the points above (or I assume so), the best thing you can do is format your system and then reinstall the Operating System (and if you use an ISO image then make sure it's a clean one). The reason you'll want to format first as opposed to just reinstall the OS through recovery (e.g. on Windows 10 you have that option) is simply due to more advanced malware being able to stay on a software-level and return back after an OS re-installation (without the need to have any firmware-infection components) - that being said, such an incident is extremely rare and I never experienced it before myself, even when I was getting daily infections for several years back at the peak years of rootkits, bootkits, and other similar dangerous threats.
I also recommend using the advice from
@SHvFl since keeping a full system image back-up is one of the best safety measures you can take; if you get infected then revert back using the backup. Backups are especially useful in the case of a virus or ransomware situation, where the only ways to retrieve your files back would be to disinfect or decrypt your files, which is highly unlikely to be a successful procedure (although it does depend on multiple factors).
Malware analysis can help identify malicious software being installed on the system, but it certainly cannot ensure that no malware is running on the system - malware can work with a device driver and then terminate it's user-mode processes for conceal purposes, or even hide it's user-mode processes through the use of API hooking (either kernel-mode or user-mode) or DKOM (Direct Kernel Object Manipulation - x86 OS only due to PatchGuard/Kernel Patch Protection). Alongside this, malicious software can compromise other running processes through the use of code injection (allocate memory into another process, then write to the newly allocated memory and finish things off by creating a remote thread within the address space of that process to get it's code executing - even better, it can work with dynamic forking).
Malware is constantly evolving, I expect to see malware in the wild which will work the hyper-visor to perform full system-wide virtualization, allowing a rootkit component to literally control everything, even on x64 systems regardless of PatchGuard/Kernel Patch Protection within the next 4-5 years. If we are all learning and security vendor engineers are all learning, nothing is stopping the malware authors from learning as-well.
IMO using tools for such things is simply unreliable, just format and re-install the OS.
Stay safe,
Wave.