How are Windows MachineKey Container File Name's Derived?

To solve your problem of finding which certificate goes with which key file for the purpose of modifying file system ACLs on the private key files, use this:

PS C:\Users\Ryan> $Cert = Get-Item Cert:\LocalMachine\My\2F6CB7D56BAA752BCCC0829DD829C0E2662FA1C6    

PS C:\Users\Ryan> $Cert.PrivateKey.CspKeyContainerInfo.UniqueKeyContainerName

fad662b360941f26a1193357aab3c12d_03f917b5-cb8b-45bd-b884-41c139a66ff7

The file naming convention is x_y, where x is a random GUID to uniquely identify the key, and y is the machine GUID found at HKLM\SOFTWARE\Microsoft\Cryptography.

Some of these unique identifiers are well-known, such as some of these IIS ones:

6de9cb26d2b98c01ec4e9e8b34824aa2_GUID      iisConfigurationKey

d6d986f09a1ee04e24c949879fdb506c_GUID      NetFrameworkConfigurationKey

76944fb33636aeddb9590521c2e8815a_GUID      iisWasKey

But others are generated randomly.

Note that this information only applies to "Local Computer" or "Machine" certificates/keys. User certificates are stored in the corresponding user-specific locations on the file system and registry.

Ryan Ries provided only partial solution, because it won't work on CNG keys. The following code will retrieve container name (hence, file name too) for CNG keys:

$signature = @"
[DllImport("Crypt32.dll", SetLastError = true, CharSet = CharSet.Auto)]
public static extern bool CertGetCertificateContextProperty(
    IntPtr pCertContext,
    uint dwPropId,
    IntPtr pvData,
    ref uint pcbData
);
[StructLayout(LayoutKind.Sequential, CharSet=CharSet.Unicode)]
public struct CRYPT_KEY_PROV_INFO {
    [MarshalAs(UnmanagedType.LPWStr)]
    public string pwszContainerName;
    [MarshalAs(UnmanagedType.LPWStr)]
    public string pwszProvName;
    public uint dwProvType;
    public uint dwFlags;
    public uint cProvParam;
    public IntPtr rgProvParam;
    public uint dwKeySpec;
}
[DllImport("ncrypt.dll", SetLastError = true)]
public static extern int NCryptOpenStorageProvider(
    ref IntPtr phProvider,
    [MarshalAs(UnmanagedType.LPWStr)]
    string pszProviderName,
    uint dwFlags
);
[DllImport("ncrypt.dll", SetLastError = true)]
public static extern int NCryptOpenKey(
    IntPtr hProvider,
    ref IntPtr phKey,
    [MarshalAs(UnmanagedType.LPWStr)]
    string pszKeyName,
    uint dwLegacyKeySpec,
    uint dwFlags
);
[DllImport("ncrypt.dll", SetLastError = true)]
public static extern int NCryptGetProperty(
    IntPtr hObject,
    [MarshalAs(UnmanagedType.LPWStr)]
    string pszProperty,
    byte[] pbOutput,
    int cbOutput,
    ref int pcbResult,
    int dwFlags
);
[DllImport("ncrypt.dll", CharSet=CharSet.Auto, SetLastError=true)]
public static extern int NCryptFreeObject(
    IntPtr hObject
);
"@
Add-Type -MemberDefinition $signature -Namespace PKI -Name Tools

$CERT_KEY_PROV_INFO_PROP_ID = 0x2 # from Wincrypt.h header file
$cert = dir cert:\currentuser\my\C541C66F490413302C845A440AFA24E98A231C3C
$pcbData = 0
[void][PKI.Tools]::CertGetCertificateContextProperty($cert.Handle,$CERT_KEY_PROV_INFO_PROP_ID,[IntPtr]::Zero,[ref]$pcbData)
$pvData = [Runtime.InteropServices.Marshal]::AllocHGlobal($pcbData)
[PKI.Tools]::CertGetCertificateContextProperty($cert.Handle,$CERT_KEY_PROV_INFO_PROP_ID,$pvData,[ref]$pcbData)
$keyProv = [Runtime.InteropServices.Marshal]::PtrToStructure($pvData,[type][PKI.Tools+CRYPT_KEY_PROV_INFO])
[Runtime.InteropServices.Marshal]::FreeHGlobal($pvData)
$phProvider = [IntPtr]::Zero
[void][PKI.Tools]::NCryptOpenStorageProvider([ref]$phProvider,$keyProv.pwszProvName,0)
$phKey = [IntPtr]::Zero
[void][PKI.Tools]::NCryptOpenKey($phProvider,[ref]$phKey,$keyProv.pwszContainerName,0,0)
$pcbResult = 0
[void][PKI.Tools]::NCryptGetProperty($phKey,"Unique Name",$null,0,[ref]$pcbResult,0)
$pbOutput = New-Object byte[] -ArgumentList $pcbResult
[void][PKI.Tools]::NCryptGetProperty($phKey,"Unique Name",$pbOutput,$pbOutput.length,[ref]$pcbResult,0)
[Text.Encoding]::Unicode.GetString($pbOutput)
[void][PKI.Tools]::NCryptFreeObject($phProvider)
[void][PKI.Tools]::NCryptFreeObject($phKey)